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{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'values'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'block', 'children': ['6', '20']}; {'id': '6', 'type': 'function_definition', 'children': ['7', '8', '10']}; {'id': '7', 'type': 'function_name', 'children': [], 'value': 'key'}; {'id': '8', 'type': 'parameters', 'children': ['9']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'th'}; {'id': '10', 'type': 'block', 'children': ['11']}; {'id': '11', 'type': 'return_statement', 'children': ['12']}; {'id': '12', 'type': 'call', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '14', 'type': 'argument_list', 'children': ['15']}; {'id': '15', 'type': 'attribute', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'th'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': '__class__'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': '__mro__'}; {'id': '20', 'type': 'return_statement', 'children': ['21']}; {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '23', 'type': 'argument_list', 'children': ['24', '30', '33']}; {'id': '24', 'type': 'call', 'children': ['25', '28']}; {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '28', 'type': 'argument_list', 'children': ['29']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '30', 'type': 'keyword_argument', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '33', 'type': 'keyword_argument', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '35', 'type': 'True', 'children': []} | def values(self):
def key(th):
return len(th.__class__.__mro__)
return sorted(dict.values(self), key=key, reverse=True) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'topological_sort'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'block', 'children': ['6', '12', '16', '26', '42', '48', '66', '70', '117']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '9', 'type': 'attribute', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}; {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'in_degree'}; {'id': '15', 'type': 'dictionary', 'children': []}; {'id': '16', 'type': 'for_statement', 'children': ['17', '18', '19']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '19', 'type': 'block', 'children': ['20']}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}; {'id': '21', 'type': 'assignment', 'children': ['22', '25']}; {'id': '22', 'type': 'subscript', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'in_degree'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '25', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '26', 'type': 'for_statement', 'children': ['27', '28', '29']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'for_statement', 'children': ['31', '32', '35']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '32', 'type': 'subscript', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '35', 'type': 'block', 'children': ['36']}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}; {'id': '37', 'type': 'augmented_assignment', 'children': ['38', '41'], 'value': '+='}; {'id': '38', 'type': 'subscript', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'in_degree'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '41', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'queue'}; {'id': '45', 'type': 'call', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'deque'}; {'id': '47', 'type': 'argument_list', 'children': []}; {'id': '48', 'type': 'for_statement', 'children': ['49', '50', '51']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'in_degree'}; {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'if_statement', 'children': ['53', '58']}; {'id': '53', 'type': 'comparison_operator', 'children': ['54', '57'], 'value': '=='}; {'id': '54', 'type': 'subscript', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'in_degree'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '57', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '58', 'type': 'block', 'children': ['59']}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'call', 'children': ['61', '64']}; {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'queue'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'appendleft'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'sorted_graph'}; {'id': '69', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '70', 'type': 'while_statement', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'queue'}; {'id': '72', 'type': 'block', 'children': ['73', '81', '88']}; {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '76', 'type': 'call', 'children': ['77', '80']}; {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'queue'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '80', 'type': 'argument_list', 'children': []}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'sorted_graph'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '88', 'type': 'for_statement', 'children': ['89', '90', '96']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '90', 'type': 'call', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '92', 'type': 'argument_list', 'children': ['93']}; {'id': '93', 'type': 'subscript', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '96', 'type': 'block', 'children': ['97', '103']}; {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'augmented_assignment', 'children': ['99', '102'], 'value': '-='}; {'id': '99', 'type': 'subscript', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'in_degree'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '102', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '103', 'type': 'if_statement', 'children': ['104', '109']}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '108'], 'value': '=='}; {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'in_degree'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '108', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}; {'id': '111', 'type': 'call', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'queue'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'appendleft'}; {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '117', 'type': 'if_statement', 'children': ['118', '127', '130']}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '123'], 'value': '=='}; {'id': '119', 'type': 'call', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'sorted_graph'}; {'id': '123', 'type': 'call', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '125', 'type': 'argument_list', 'children': ['126']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'return_statement', 'children': ['129']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'sorted_graph'}; {'id': '130', 'type': 'else_clause', 'children': ['131']}; {'id': '131', 'type': 'block', 'children': ['132']}; {'id': '132', 'type': 'raise_statement', 'children': ['133']}; {'id': '133', 'type': 'call', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '135', 'type': 'argument_list', 'children': ['136']}; {'id': '136', 'type': 'string', 'children': [], 'value': "'graph is not acyclic'"} | def topological_sort(self):
graph = self.graph
in_degree = {}
for u in graph:
in_degree[u] = 0
for u in graph:
for v in graph[u]:
in_degree[v] += 1
queue = deque()
for u in in_degree:
if in_degree[u] == 0:
queue.appendleft(u)
sorted_graph = []
while queue:
u = queue.pop()
sorted_graph.append(u)
for v in sorted(graph[u]):
in_degree[v] -= 1
if in_degree[v] == 0:
queue.appendleft(v)
if len(sorted_graph) == len(graph):
return sorted_graph
else:
raise ValueError('graph is not acyclic') |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_music_lib_search'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'search'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'max_items'}; {'id': '8', 'type': 'block', 'children': ['9', '38', '42', '63']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '12', 'type': 'call', 'children': ['13', '18']}; {'id': '13', 'type': 'attribute', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'contentDirectory'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'Browse'}; {'id': '18', 'type': 'argument_list', 'children': ['19']}; {'id': '19', 'type': 'list', 'children': ['20', '23', '26', '29', '32', '35'], 'value': "[\n ('ObjectID', search),\n ('BrowseFlag', 'BrowseDirectChildren'),\n ('Filter', '*'),\n ('StartingIndex', start),\n ('RequestedCount', max_items),\n ('SortCriteria', '')\n ]"}; {'id': '20', 'type': 'tuple', 'children': ['21', '22']}; {'id': '21', 'type': 'string', 'children': [], 'value': "'ObjectID'"}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'search'}; {'id': '23', 'type': 'tuple', 'children': ['24', '25']}; {'id': '24', 'type': 'string', 'children': [], 'value': "'BrowseFlag'"}; {'id': '25', 'type': 'string', 'children': [], 'value': "'BrowseDirectChildren'"}; {'id': '26', 'type': 'tuple', 'children': ['27', '28']}; {'id': '27', 'type': 'string', 'children': [], 'value': "'Filter'"}; {'id': '28', 'type': 'string', 'children': [], 'value': "'*'"}; {'id': '29', 'type': 'tuple', 'children': ['30', '31']}; {'id': '30', 'type': 'string', 'children': [], 'value': "'StartingIndex'"}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '32', 'type': 'tuple', 'children': ['33', '34']}; {'id': '33', 'type': 'string', 'children': [], 'value': "'RequestedCount'"}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'max_items'}; {'id': '35', 'type': 'tuple', 'children': ['36', '37']}; {'id': '36', 'type': 'string', 'children': [], 'value': "'SortCriteria'"}; {'id': '37', 'type': 'string', 'children': [], 'value': "''"}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}; {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'metadata'}; {'id': '41', 'type': 'dictionary', 'children': []}; {'id': '42', 'type': 'for_statement', 'children': ['43', '44', '48']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '44', 'type': 'list', 'children': ['45', '46', '47'], 'value': "['NumberReturned', 'TotalMatches', 'UpdateID']"}; {'id': '45', 'type': 'string', 'children': [], 'value': "'NumberReturned'"}; {'id': '46', 'type': 'string', 'children': [], 'value': "'TotalMatches'"}; {'id': '47', 'type': 'string', 'children': [], 'value': "'UpdateID'"}; {'id': '48', 'type': 'block', 'children': ['49']}; {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '57']}; {'id': '51', 'type': 'subscript', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'metadata'}; {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'camel_to_underscore'}; {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'subscript', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '63', 'type': 'return_statement', 'children': ['64']}; {'id': '64', 'type': 'expression_list', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'metadata'} | def _music_lib_search(self, search, start, max_items):
response = self.contentDirectory.Browse([
('ObjectID', search),
('BrowseFlag', 'BrowseDirectChildren'),
('Filter', '*'),
('StartingIndex', start),
('RequestedCount', max_items),
('SortCriteria', '')
])
metadata = {}
for tag in ['NumberReturned', 'TotalMatches', 'UpdateID']:
metadata[camel_to_underscore(tag)] = int(response[tag])
return response, metadata |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'unique'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'seq'}; {'id': '5', 'type': 'block', 'children': ['6', '10', '26']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'cleaned'}; {'id': '9', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '10', 'type': 'for_statement', 'children': ['11', '12', '13']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'each'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'seq'}; {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'if_statement', 'children': ['15', '18']}; {'id': '15', 'type': 'comparison_operator', 'children': ['16', '17'], 'value': 'not'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'each'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'cleaned'}; {'id': '18', 'type': 'block', 'children': ['19']}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'call', 'children': ['21', '24']}; {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'cleaned'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'each'}; {'id': '26', 'type': 'return_statement', 'children': ['27']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'cleaned'} | def unique(seq):
cleaned = []
for each in seq:
if each not in cleaned:
cleaned.append(each)
return cleaned |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'build_schema_info'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'connection_alias'}; {'id': '5', 'type': 'block', 'children': ['6', '13', '17', '127']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'connection'}; {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'get_valid_connection'}; {'id': '11', 'type': 'argument_list', 'children': ['12']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'connection_alias'}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '16', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '17', 'type': 'with_statement', 'children': ['18', '28']}; {'id': '18', 'type': 'with_clause', 'children': ['19']}; {'id': '19', 'type': 'with_item', 'children': ['20']}; {'id': '20', 'type': 'as_pattern', 'children': ['21', '26']}; {'id': '21', 'type': 'call', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'connection'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'cursor'}; {'id': '25', 'type': 'argument_list', 'children': []}; {'id': '26', 'type': 'as_pattern_target', 'children': ['27']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'cursor'}; {'id': '28', 'type': 'block', 'children': ['29', '45']}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'tables_to_introspect'}; {'id': '32', 'type': 'call', 'children': ['33', '38']}; {'id': '33', 'type': 'attribute', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'connection'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'introspection'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'table_names'}; {'id': '38', 'type': 'argument_list', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'cursor'}; {'id': '40', 'type': 'keyword_argument', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'include_views'}; {'id': '42', 'type': 'call', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': '_include_views'}; {'id': '44', 'type': 'argument_list', 'children': []}; {'id': '45', 'type': 'for_statement', 'children': ['46', '47', '48']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'table_name'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'tables_to_introspect'}; {'id': '48', 'type': 'block', 'children': ['49', '57', '61', '73', '118']}; {'id': '49', 'type': 'if_statement', 'children': ['50', '55']}; {'id': '50', 'type': 'not_operator', 'children': ['51']}; {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': '_include_table'}; {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'table_name'}; {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'continue_statement', 'children': []}; {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'td'}; {'id': '60', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'table_description'}; {'id': '64', 'type': 'call', 'children': ['65', '70']}; {'id': '65', 'type': 'attribute', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'connection'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'introspection'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'get_table_description'}; {'id': '70', 'type': 'argument_list', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'cursor'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'table_name'}; {'id': '73', 'type': 'for_statement', 'children': ['74', '75', '76']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'table_description'}; {'id': '76', 'type': 'block', 'children': ['77', '83', '109']}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'column_name'}; {'id': '80', 'type': 'subscript', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '82', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '83', 'type': 'try_statement', 'children': ['84', '99']}; {'id': '84', 'type': 'block', 'children': ['85']}; {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'field_type'}; {'id': '88', 'type': 'call', 'children': ['89', '94']}; {'id': '89', 'type': 'attribute', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'connection'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'introspection'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'get_field_type'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '98']}; {'id': '95', 'type': 'subscript', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '97', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '99', 'type': 'except_clause', 'children': ['100', '104']}; {'id': '100', 'type': 'as_pattern', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '102', 'type': 'as_pattern_target', 'children': ['103']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '104', 'type': 'block', 'children': ['105']}; {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'assignment', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'field_type'}; {'id': '108', 'type': 'string', 'children': [], 'value': "'Unknown'"}; {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'call', 'children': ['111', '114']}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'td'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}; {'id': '115', 'type': 'tuple', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'column_name'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'field_type'}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}; {'id': '119', 'type': 'call', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '123', 'type': 'argument_list', 'children': ['124']}; {'id': '124', 'type': 'tuple', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'table_name'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'td'}; {'id': '127', 'type': 'return_statement', 'children': ['128']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'ret'} | def build_schema_info(connection_alias):
connection = get_valid_connection(connection_alias)
ret = []
with connection.cursor() as cursor:
tables_to_introspect = connection.introspection.table_names(cursor, include_views=_include_views())
for table_name in tables_to_introspect:
if not _include_table(table_name):
continue
td = []
table_description = connection.introspection.get_table_description(cursor, table_name)
for row in table_description:
column_name = row[0]
try:
field_type = connection.introspection.get_field_type(row[1], row)
except KeyError as e:
field_type = 'Unknown'
td.append((column_name, field_type))
ret.append((table_name, td))
return ret |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '15']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'fetchThreads'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'thread_location'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'before'}; {'id': '8', 'type': 'None', 'children': []}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'after'}; {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '14', 'type': 'None', 'children': []}; {'id': '15', 'type': 'block', 'children': ['16', '20', '24', '106', '154', '170']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '19', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}; {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'last_thread_timestamp'}; {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'while_statement', 'children': ['25', '26']}; {'id': '25', 'type': 'True', 'children': []}; {'id': '26', 'type': 'block', 'children': ['27', '38', '52', '71', '80']}; {'id': '27', 'type': 'if_statement', 'children': ['28', '36']}; {'id': '28', 'type': 'boolean_operator', 'children': ['29', '30'], 'value': 'and'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '30', 'type': 'comparison_operator', 'children': ['31', '35'], 'value': '>='}; {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '36', 'type': 'block', 'children': ['37']}; {'id': '37', 'type': 'break_statement', 'children': []}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}; {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'candidates'}; {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'fetchThreadList'}; {'id': '45', 'type': 'argument_list', 'children': ['46', '49']}; {'id': '46', 'type': 'keyword_argument', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'before'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'last_thread_timestamp'}; {'id': '49', 'type': 'keyword_argument', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'thread_location'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'thread_location'}; {'id': '52', 'type': 'if_statement', 'children': ['53', '59', '68']}; {'id': '53', 'type': 'comparison_operator', 'children': ['54', '58'], 'value': '>'}; {'id': '54', 'type': 'call', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'candidates'}; {'id': '58', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '59', 'type': 'block', 'children': ['60']}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}; {'id': '61', 'type': 'augmented_assignment', 'children': ['62', '63'], 'value': '+='}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '63', 'type': 'subscript', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'candidates'}; {'id': '65', 'type': 'slice', 'children': ['66', '67']}; {'id': '66', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '67', 'type': 'colon', 'children': []}; {'id': '68', 'type': 'else_clause', 'children': ['69']}; {'id': '69', 'type': 'block', 'children': ['70']}; {'id': '70', 'type': 'break_statement', 'children': []}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'last_thread_timestamp'}; {'id': '74', 'type': 'attribute', 'children': ['75', '79']}; {'id': '75', 'type': 'subscript', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '77', 'type': 'unary_operator', 'children': ['78'], 'value': '-'}; {'id': '78', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'last_message_timestamp'}; {'id': '80', 'type': 'if_statement', 'children': ['81', '104']}; {'id': '81', 'type': 'boolean_operator', 'children': ['82', '93'], 'value': 'or'}; {'id': '82', 'type': '()', 'children': ['83']}; {'id': '83', 'type': 'boolean_operator', 'children': ['84', '87'], 'value': 'and'}; {'id': '84', 'type': 'comparison_operator', 'children': ['85', '86'], 'value': 'is'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'before'}; {'id': '86', 'type': 'None', 'children': []}; {'id': '87', 'type': 'comparison_operator', 'children': ['88', '92'], 'value': '>'}; {'id': '88', 'type': 'call', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'last_thread_timestamp'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'before'}; {'id': '93', 'type': '()', 'children': ['94']}; {'id': '94', 'type': 'boolean_operator', 'children': ['95', '98'], 'value': 'and'}; {'id': '95', 'type': 'comparison_operator', 'children': ['96', '97'], 'value': 'is'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'after'}; {'id': '97', 'type': 'None', 'children': []}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '103'], 'value': '<'}; {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '101', 'type': 'argument_list', 'children': ['102']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'last_thread_timestamp'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'after'}; {'id': '104', 'type': 'block', 'children': ['105']}; {'id': '105', 'type': 'break_statement', 'children': []}; {'id': '106', 'type': 'if_statement', 'children': ['107', '114']}; {'id': '107', 'type': 'boolean_operator', 'children': ['108', '111'], 'value': 'or'}; {'id': '108', 'type': 'comparison_operator', 'children': ['109', '110'], 'value': 'is'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'before'}; {'id': '110', 'type': 'None', 'children': []}; {'id': '111', 'type': 'comparison_operator', 'children': ['112', '113'], 'value': 'is'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'after'}; {'id': '113', 'type': 'None', 'children': []}; {'id': '114', 'type': 'block', 'children': ['115']}; {'id': '115', 'type': 'for_statement', 'children': ['116', '117', '118']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '118', 'type': 'block', 'children': ['119', '128']}; {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'last_message_timestamp'}; {'id': '122', 'type': 'call', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}; {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'last_message_timestamp'}; {'id': '128', 'type': 'if_statement', 'children': ['129', '146']}; {'id': '129', 'type': 'boolean_operator', 'children': ['130', '138'], 'value': 'or'}; {'id': '130', 'type': '()', 'children': ['131']}; {'id': '131', 'type': 'boolean_operator', 'children': ['132', '135'], 'value': 'and'}; {'id': '132', 'type': 'comparison_operator', 'children': ['133', '134'], 'value': 'is'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'before'}; {'id': '134', 'type': 'None', 'children': []}; {'id': '135', 'type': 'comparison_operator', 'children': ['136', '137'], 'value': '>'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'last_message_timestamp'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'before'}; {'id': '138', 'type': '()', 'children': ['139']}; {'id': '139', 'type': 'boolean_operator', 'children': ['140', '143'], 'value': 'and'}; {'id': '140', 'type': 'comparison_operator', 'children': ['141', '142'], 'value': 'is'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'after'}; {'id': '142', 'type': 'None', 'children': []}; {'id': '143', 'type': 'comparison_operator', 'children': ['144', '145'], 'value': '<'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'last_message_timestamp'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'after'}; {'id': '146', 'type': 'block', 'children': ['147']}; {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'call', 'children': ['149', '152']}; {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'remove'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '154', 'type': 'if_statement', 'children': ['155', '163']}; {'id': '155', 'type': 'boolean_operator', 'children': ['156', '157'], 'value': 'and'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '157', 'type': 'comparison_operator', 'children': ['158', '162'], 'value': '>'}; {'id': '158', 'type': 'call', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '163', 'type': 'block', 'children': ['164']}; {'id': '164', 'type': 'return_statement', 'children': ['165']}; {'id': '165', 'type': 'subscript', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '167', 'type': 'slice', 'children': ['168', '169']}; {'id': '168', 'type': 'colon', 'children': []}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '170', 'type': 'return_statement', 'children': ['171']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'threads'} | def fetchThreads(self, thread_location, before=None, after=None, limit=None):
threads = []
last_thread_timestamp = None
while True:
if limit and len(threads) >= limit:
break
candidates = self.fetchThreadList(
before=last_thread_timestamp, thread_location=thread_location
)
if len(candidates) > 1:
threads += candidates[1:]
else:
break
last_thread_timestamp = threads[-1].last_message_timestamp
if (before is not None and int(last_thread_timestamp) > before) or (
after is not None and int(last_thread_timestamp) < after
):
break
if before is not None or after is not None:
for t in threads:
last_message_timestamp = int(t.last_message_timestamp)
if (before is not None and last_message_timestamp > before) or (
after is not None and last_message_timestamp < after
):
threads.remove(t)
if limit and len(threads) > limit:
return threads[:limit]
return threads |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_key_value'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'is_hll'}; {'id': '8', 'type': 'False', 'children': []}; {'id': '9', 'type': 'block', 'children': ['10', '12']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}; {'id': '11', 'type': 'string', 'children': [], 'value': "'''\n Returns the proper key value for the stats\n @param key: the redis key\n @param is_hll: the key is a HyperLogLog, else is a sorted set\n '''"}; {'id': '12', 'type': 'if_statement', 'children': ['13', '14', '25']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'is_hll'}; {'id': '14', 'type': 'block', 'children': ['15']}; {'id': '15', 'type': 'return_statement', 'children': ['16']}; {'id': '16', 'type': 'call', 'children': ['17', '22']}; {'id': '17', 'type': 'attribute', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'redis_conn'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'execute_command'}; {'id': '22', 'type': 'argument_list', 'children': ['23', '24']}; {'id': '23', 'type': 'string', 'children': [], 'value': '"PFCOUNT"'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '25', 'type': 'else_clause', 'children': ['26']}; {'id': '26', 'type': 'block', 'children': ['27']}; {'id': '27', 'type': 'return_statement', 'children': ['28']}; {'id': '28', 'type': 'call', 'children': ['29', '34']}; {'id': '29', 'type': 'attribute', 'children': ['30', '33']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'redis_conn'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'zcard'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'key'} | def _get_key_value(self, key, is_hll=False):
'''
Returns the proper key value for the stats
@param key: the redis key
@param is_hll: the key is a HyperLogLog, else is a sorted set
'''
if is_hll:
return self.redis_conn.execute_command("PFCOUNT", key)
else:
return self.redis_conn.zcard(key) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_bin'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '6', 'type': 'block', 'children': ['7', '9', '13', '62']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'string', 'children': [], 'value': "'''\n Returns a binned dictionary based on redis zscore\n @return: The sorted dict\n '''"}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'sortedDict'}; {'id': '12', 'type': 'dictionary', 'children': []}; {'id': '13', 'type': 'for_statement', 'children': ['14', '15', '23']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '15', 'type': 'call', 'children': ['16', '21']}; {'id': '16', 'type': 'attribute', 'children': ['17', '20']}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'redis_conn'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'zscan_iter'}; {'id': '21', 'type': 'argument_list', 'children': ['22']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '23', 'type': 'block', 'children': ['24', '35', '42', '53']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}; {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'my_item'}; {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'ujson'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'loads'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'subscript', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '34', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'my_score'}; {'id': '38', 'type': 'unary_operator', 'children': ['39'], 'value': '-'}; {'id': '39', 'type': 'subscript', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '41', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '42', 'type': 'if_statement', 'children': ['43', '46']}; {'id': '43', 'type': 'comparison_operator', 'children': ['44', '45'], 'value': 'not'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'my_score'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'sortedDict'}; {'id': '46', 'type': 'block', 'children': ['47']}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '52']}; {'id': '49', 'type': 'subscript', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'sortedDict'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'my_score'}; {'id': '52', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '60']}; {'id': '55', 'type': 'attribute', 'children': ['56', '59']}; {'id': '56', 'type': 'subscript', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'sortedDict'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'my_score'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'my_item'}; {'id': '62', 'type': 'return_statement', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'sortedDict'} | def _get_bin(self, key):
'''
Returns a binned dictionary based on redis zscore
@return: The sorted dict
'''
sortedDict = {}
for item in self.redis_conn.zscan_iter(key):
my_item = ujson.loads(item[0])
my_score = -item[1]
if my_score not in sortedDict:
sortedDict[my_score] = []
sortedDict[my_score].append(my_item)
return sortedDict |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_is_viable_phone_number'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'number'}; {'id': '5', 'type': 'block', 'children': ['6', '16', '24']}; {'id': '6', 'type': 'if_statement', 'children': ['7', '13']}; {'id': '7', 'type': 'comparison_operator', 'children': ['8', '12'], 'value': '<'}; {'id': '8', 'type': 'call', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '10', 'type': 'argument_list', 'children': ['11']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'number'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': '_MIN_LENGTH_FOR_NSN'}; {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'return_statement', 'children': ['15']}; {'id': '15', 'type': 'False', 'children': []}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '19', 'type': 'call', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'fullmatch'}; {'id': '21', 'type': 'argument_list', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': '_VALID_PHONE_NUMBER_PATTERN'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'number'}; {'id': '24', 'type': 'return_statement', 'children': ['25']}; {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'bool'}; {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'match'} | def _is_viable_phone_number(number):
if len(number) < _MIN_LENGTH_FOR_NSN:
return False
match = fullmatch(_VALID_PHONE_NUMBER_PATTERN, number)
return bool(match) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '__encoded_params_for_signature'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '6', 'type': 'block', 'children': ['7', '109']}; {'id': '7', 'type': 'function_definition', 'children': ['8', '9', '11']}; {'id': '8', 'type': 'function_name', 'children': [], 'value': 'encoded_pairs'}; {'id': '9', 'type': 'parameters', 'children': ['10']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '11', 'type': 'block', 'children': ['12']}; {'id': '12', 'type': 'for_statement', 'children': ['13', '16', '22']}; {'id': '13', 'type': 'pattern_list', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '16', 'type': 'call', 'children': ['17', '20']}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'six'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'iteritems'}; {'id': '20', 'type': 'argument_list', 'children': ['21']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '22', 'type': 'block', 'children': ['23', '29', '62', '81', '94']}; {'id': '23', 'type': 'if_statement', 'children': ['24', '27']}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '26'], 'value': '=='}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '26', 'type': 'string', 'children': [], 'value': "'hmac'"}; {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'continue_statement', 'children': []}; {'id': '29', 'type': 'if_statement', 'children': ['30', '36']}; {'id': '30', 'type': 'call', 'children': ['31', '34']}; {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}; {'id': '35', 'type': 'string', 'children': [], 'value': "'[]'"}; {'id': '36', 'type': 'block', 'children': ['37', '46']}; {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '40', 'type': 'call', 'children': ['41', '44']}; {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'rstrip'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'string', 'children': [], 'value': "'[]'"}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'dumps'}; {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}; {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '59', 'type': 'argument_list', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}; {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '65', 'type': 'call', 'children': ['66', '78']}; {'id': '66', 'type': 'attribute', 'children': ['67', '77']}; {'id': '67', 'type': 'call', 'children': ['68', '74']}; {'id': '68', 'type': 'attribute', 'children': ['69', '73']}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '74', 'type': 'argument_list', 'children': ['75', '76']}; {'id': '75', 'type': 'string', 'children': [], 'value': '"%"'}; {'id': '76', 'type': 'string', 'children': [], 'value': '"%25"'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '78', 'type': 'argument_list', 'children': ['79', '80']}; {'id': '79', 'type': 'string', 'children': [], 'value': '"="'}; {'id': '80', 'type': 'string', 'children': [], 'value': '"%3D"'}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '84', 'type': 'call', 'children': ['85', '91']}; {'id': '85', 'type': 'attribute', 'children': ['86', '90']}; {'id': '86', 'type': 'call', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '91', 'type': 'argument_list', 'children': ['92', '93']}; {'id': '92', 'type': 'string', 'children': [], 'value': '"%"'}; {'id': '93', 'type': 'string', 'children': [], 'value': '"%25"'}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'yield', 'children': ['96']}; {'id': '96', 'type': 'call', 'children': ['97', '106']}; {'id': '97', 'type': 'attribute', 'children': ['98', '105']}; {'id': '98', 'type': 'call', 'children': ['99', '102']}; {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'string', 'children': [], 'value': "'{0}={1}'"}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '102', 'type': 'argument_list', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '106', 'type': 'argument_list', 'children': ['107', '108']}; {'id': '107', 'type': 'string', 'children': [], 'value': '"&"'}; {'id': '108', 'type': 'string', 'children': [], 'value': '"%26"'}; {'id': '109', 'type': 'return_statement', 'children': ['110']}; {'id': '110', 'type': 'call', 'children': ['111', '114']}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'string', 'children': [], 'value': '"&"'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}; {'id': '115', 'type': 'call', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'call', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'encoded_pairs'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'params'} | def __encoded_params_for_signature(cls, params):
def encoded_pairs(params):
for k, v in six.iteritems(params):
if k == 'hmac':
continue
if k.endswith('[]'):
k = k.rstrip('[]')
v = json.dumps(list(map(str, v)))
k = str(k).replace("%", "%25").replace("=", "%3D")
v = str(v).replace("%", "%25")
yield '{0}={1}'.format(k, v).replace("&", "%26")
return "&".join(sorted(encoded_pairs(params))) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'group_keys'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'block', 'children': ['6']}; {'id': '6', 'type': 'for_statement', 'children': ['7', '8', '20']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '8', 'type': 'call', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '10', 'type': 'argument_list', 'children': ['11']}; {'id': '11', 'type': 'call', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'listdir'}; {'id': '13', 'type': 'argument_list', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': '_store'}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': '_path'}; {'id': '20', 'type': 'block', 'children': ['21', '29']}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '24', 'type': 'binary_operator', 'children': ['25', '28'], 'value': '+'}; {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': '_key_prefix'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '29', 'type': 'if_statement', 'children': ['30', '37']}; {'id': '30', 'type': 'call', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'contains_group'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '36']}; {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': '_store'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '37', 'type': 'block', 'children': ['38']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}; {'id': '39', 'type': 'yield', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'key'} | def group_keys(self):
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if contains_group(self._store, path):
yield key |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'array_keys'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'block', 'children': ['6']}; {'id': '6', 'type': 'for_statement', 'children': ['7', '8', '20']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '8', 'type': 'call', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '10', 'type': 'argument_list', 'children': ['11']}; {'id': '11', 'type': 'call', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'listdir'}; {'id': '13', 'type': 'argument_list', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': '_store'}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': '_path'}; {'id': '20', 'type': 'block', 'children': ['21', '29']}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '24', 'type': 'binary_operator', 'children': ['25', '28'], 'value': '+'}; {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': '_key_prefix'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '29', 'type': 'if_statement', 'children': ['30', '37']}; {'id': '30', 'type': 'call', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'contains_array'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '36']}; {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': '_store'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '37', 'type': 'block', 'children': ['38']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}; {'id': '39', 'type': 'yield', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'key'} | def array_keys(self):
for key in sorted(listdir(self._store, self._path)):
path = self._key_prefix + key
if contains_array(self._store, path):
yield key |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '36']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'init_array'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18', '21', '24', '27', '30', '33']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'store'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '8', 'type': 'True', 'children': []}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'compressor'}; {'id': '14', 'type': 'string', 'children': [], 'value': "'default'"}; {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'default_parameter', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'order'}; {'id': '20', 'type': 'string', 'children': [], 'value': "'C'"}; {'id': '21', 'type': 'default_parameter', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'overwrite'}; {'id': '23', 'type': 'False', 'children': []}; {'id': '24', 'type': 'default_parameter', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '26', 'type': 'None', 'children': []}; {'id': '27', 'type': 'default_parameter', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'chunk_store'}; {'id': '29', 'type': 'None', 'children': []}; {'id': '30', 'type': 'default_parameter', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '32', 'type': 'None', 'children': []}; {'id': '33', 'type': 'default_parameter', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'object_codec'}; {'id': '35', 'type': 'None', 'children': []}; {'id': '36', 'type': 'block', 'children': ['37', '44', '58']}; {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '40', 'type': 'call', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'normalize_storage_path'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}; {'id': '45', 'type': 'call', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': '_require_parent_group'}; {'id': '47', 'type': 'argument_list', 'children': ['48', '49', '52', '55']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '49', 'type': 'keyword_argument', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'store'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'store'}; {'id': '52', 'type': 'keyword_argument', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'chunk_store'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'chunk_store'}; {'id': '55', 'type': 'keyword_argument', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'overwrite'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'overwrite'}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}; {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': '_init_array_metadata'}; {'id': '61', 'type': 'argument_list', 'children': ['62', '63', '66', '69', '72', '75', '78', '81', '84', '87', '90', '93']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'store'}; {'id': '63', 'type': 'keyword_argument', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '66', 'type': 'keyword_argument', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '69', 'type': 'keyword_argument', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '72', 'type': 'keyword_argument', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'compressor'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'compressor'}; {'id': '75', 'type': 'keyword_argument', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '78', 'type': 'keyword_argument', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'order'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'order'}; {'id': '81', 'type': 'keyword_argument', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'overwrite'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'overwrite'}; {'id': '84', 'type': 'keyword_argument', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '87', 'type': 'keyword_argument', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'chunk_store'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'chunk_store'}; {'id': '90', 'type': 'keyword_argument', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '93', 'type': 'keyword_argument', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'object_codec'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'object_codec'} | def init_array(store, shape, chunks=True, dtype=None, compressor='default',
fill_value=None, order='C', overwrite=False, path=None,
chunk_store=None, filters=None, object_codec=None):
path = normalize_storage_path(path)
_require_parent_group(path, store=store, chunk_store=chunk_store, overwrite=overwrite)
_init_array_metadata(store, shape=shape, chunks=chunks, dtype=dtype,
compressor=compressor, fill_value=fill_value,
order=order, overwrite=overwrite, path=path,
chunk_store=chunk_store, filters=filters,
object_codec=object_codec) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '26']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'view'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20', '23']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '16', 'type': 'None', 'children': []}; {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'read_only'}; {'id': '22', 'type': 'None', 'children': []}; {'id': '23', 'type': 'default_parameter', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'synchronizer'}; {'id': '25', 'type': 'None', 'children': []}; {'id': '26', 'type': 'block', 'children': ['27', '33', '39', '45', '56', '67', '91', '97', '125', '151', '173', '184', '195']}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'store'}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': '_store'}; {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'chunk_store'}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': '_chunk_store'}; {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'id': '40', 'type': 'assignment', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': '_path'}; {'id': '45', 'type': 'if_statement', 'children': ['46', '49']}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '48'], 'value': 'is'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'read_only'}; {'id': '48', 'type': 'None', 'children': []}; {'id': '49', 'type': 'block', 'children': ['50']}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}; {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'read_only'}; {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': '_read_only'}; {'id': '56', 'type': 'if_statement', 'children': ['57', '60']}; {'id': '57', 'type': 'comparison_operator', 'children': ['58', '59'], 'value': 'is'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'synchronizer'}; {'id': '59', 'type': 'None', 'children': []}; {'id': '60', 'type': 'block', 'children': ['61']}; {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'synchronizer'}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': '_synchronizer'}; {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '70', 'type': 'call', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'Array'}; {'id': '72', 'type': 'argument_list', 'children': ['73', '76', '79', '82', '85', '88']}; {'id': '73', 'type': 'keyword_argument', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'store'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'store'}; {'id': '76', 'type': 'keyword_argument', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '79', 'type': 'keyword_argument', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'chunk_store'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'chunk_store'}; {'id': '82', 'type': 'keyword_argument', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'read_only'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'read_only'}; {'id': '85', 'type': 'keyword_argument', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'synchronizer'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'synchronizer'}; {'id': '88', 'type': 'keyword_argument', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'cache_metadata'}; {'id': '90', 'type': 'True', 'children': []}; {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '96']}; {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': '_is_view'}; {'id': '96', 'type': 'True', 'children': []}; {'id': '97', 'type': 'if_statement', 'children': ['98', '101', '108']}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '100'], 'value': 'is'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '100', 'type': 'None', 'children': []}; {'id': '101', 'type': 'block', 'children': ['102']}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': '_dtype'}; {'id': '108', 'type': 'else_clause', 'children': ['109']}; {'id': '109', 'type': 'block', 'children': ['110', '119']}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}; {'id': '111', 'type': 'assignment', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '113', 'type': 'call', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '124']}; {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': '_dtype'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '125', 'type': 'if_statement', 'children': ['126', '129', '136']}; {'id': '126', 'type': 'comparison_operator', 'children': ['127', '128'], 'value': 'is'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '128', 'type': 'None', 'children': []}; {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}; {'id': '131', 'type': 'assignment', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': '_shape'}; {'id': '136', 'type': 'else_clause', 'children': ['137']}; {'id': '137', 'type': 'block', 'children': ['138', '145']}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}; {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '141', 'type': 'call', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'normalize_shape'}; {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '150']}; {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': '_shape'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '151', 'type': 'if_statement', 'children': ['152', '155']}; {'id': '152', 'type': 'comparison_operator', 'children': ['153', '154'], 'value': 'is'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '154', 'type': 'None', 'children': []}; {'id': '155', 'type': 'block', 'children': ['156', '167']}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}; {'id': '157', 'type': 'assignment', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '159', 'type': 'call', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'normalize_chunks'}; {'id': '161', 'type': 'argument_list', 'children': ['162', '163', '164']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'itemsize'}; {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'assignment', 'children': ['169', '172']}; {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': '_chunks'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '173', 'type': 'if_statement', 'children': ['174', '177']}; {'id': '174', 'type': 'comparison_operator', 'children': ['175', '176'], 'value': 'is'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '176', 'type': 'None', 'children': []}; {'id': '177', 'type': 'block', 'children': ['178']}; {'id': '178', 'type': 'expression_statement', 'children': ['179']}; {'id': '179', 'type': 'assignment', 'children': ['180', '183']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': '_fill_value'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '184', 'type': 'if_statement', 'children': ['185', '188']}; {'id': '185', 'type': 'comparison_operator', 'children': ['186', '187'], 'value': 'is'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '187', 'type': 'None', 'children': []}; {'id': '188', 'type': 'block', 'children': ['189']}; {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'assignment', 'children': ['191', '194']}; {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': '_filters'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '195', 'type': 'return_statement', 'children': ['196']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'a'} | def view(self, shape=None, chunks=None, dtype=None,
fill_value=None, filters=None, read_only=None,
synchronizer=None):
store = self._store
chunk_store = self._chunk_store
path = self._path
if read_only is None:
read_only = self._read_only
if synchronizer is None:
synchronizer = self._synchronizer
a = Array(store=store, path=path, chunk_store=chunk_store, read_only=read_only,
synchronizer=synchronizer, cache_metadata=True)
a._is_view = True
if dtype is None:
dtype = self._dtype
else:
dtype = np.dtype(dtype)
a._dtype = dtype
if shape is None:
shape = self._shape
else:
shape = normalize_shape(shape)
a._shape = shape
if chunks is not None:
chunks = normalize_chunks(chunks, shape, dtype.itemsize)
a._chunks = chunks
if fill_value is not None:
a._fill_value = fill_value
if filters is not None:
a._filters = filters
return a |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'image_field_data'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'include_empty_option'}; {'id': '7', 'type': 'False', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '37', '51', '61', '93', '105']}; {'id': '9', 'type': 'try_statement', 'children': ['10', '23']}; {'id': '10', 'type': 'block', 'children': ['11']}; {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'images'}; {'id': '14', 'type': 'call', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'get_available_images'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '18', 'type': 'attribute', 'children': ['19', '22']}; {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'project_id'}; {'id': '23', 'type': 'except_clause', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '25', 'type': 'block', 'children': ['26']}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'exceptions'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'handle'}; {'id': '31', 'type': 'argument_list', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'string', 'children': [], 'value': "'Unable to retrieve images'"}; {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'call', 'children': ['39', '42']}; {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'images'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}; {'id': '43', 'type': 'keyword_argument', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '45', 'type': 'lambda', 'children': ['46', '48']}; {'id': '46', 'type': 'lambda_parameters', 'children': ['47']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'images_list'}; {'id': '54', 'type': 'list', 'children': ['55'], 'value': "[('', _('Select Image'))]"}; {'id': '55', 'type': 'tuple', 'children': ['56', '57']}; {'id': '56', 'type': 'string', 'children': [], 'value': "''"}; {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'string', 'children': [], 'value': "'Select Image'"}; {'id': '61', 'type': 'for_statement', 'children': ['62', '63', '64']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'images'}; {'id': '64', 'type': 'block', 'children': ['65', '82']}; {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'image_label'}; {'id': '68', 'type': 'call', 'children': ['69', '72']}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'string', 'children': [], 'value': 'u"{} ({})"'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '72', 'type': 'argument_list', 'children': ['73', '76']}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '76', 'type': 'call', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'filesizeformat'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}; {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'size'}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}; {'id': '83', 'type': 'call', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'images_list'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'tuple', 'children': ['89', '92']}; {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'image_label'}; {'id': '93', 'type': 'if_statement', 'children': ['94', '96']}; {'id': '94', 'type': 'not_operator', 'children': ['95']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'images'}; {'id': '96', 'type': 'block', 'children': ['97']}; {'id': '97', 'type': 'return_statement', 'children': ['98']}; {'id': '98', 'type': 'list', 'children': ['99'], 'value': '[("", _("No images available")), ]'}; {'id': '99', 'type': 'tuple', 'children': ['100', '101']}; {'id': '100', 'type': 'string', 'children': [], 'value': '""'}; {'id': '101', 'type': 'call', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'string', 'children': [], 'value': '"No images available"'}; {'id': '105', 'type': 'return_statement', 'children': ['106']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'images_list'} | def image_field_data(request, include_empty_option=False):
try:
images = get_available_images(request, request.user.project_id)
except Exception:
exceptions.handle(request, _('Unable to retrieve images'))
images.sort(key=lambda c: c.name)
images_list = [('', _('Select Image'))]
for image in images:
image_label = u"{} ({})".format(image.name, filesizeformat(image.size))
images_list.append((image.id, image_label))
if not images:
return [("", _("No images available")), ]
return images_list |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_flavor_list'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'flavors'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'with_menu_label'}; {'id': '8', 'type': 'True', 'children': []}; {'id': '9', 'type': 'block', 'children': ['10', '43']}; {'id': '10', 'type': 'function_definition', 'children': ['11', '12', '15']}; {'id': '11', 'type': 'function_name', 'children': [], 'value': 'get_key'}; {'id': '12', 'type': 'parameters', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'flavor'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '15', 'type': 'block', 'children': ['16']}; {'id': '16', 'type': 'try_statement', 'children': ['17', '24']}; {'id': '17', 'type': 'block', 'children': ['18']}; {'id': '18', 'type': 'return_statement', 'children': ['19']}; {'id': '19', 'type': 'call', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '21', 'type': 'argument_list', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'flavor'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '24', 'type': 'except_clause', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}; {'id': '26', 'type': 'block', 'children': ['27', '37']}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'call', 'children': ['29', '32']}; {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'LOG'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '36']}; {'id': '33', 'type': 'concatenated_string', 'children': ['34', '35']}; {'id': '34', 'type': 'string', 'children': [], 'value': '\'Could not find sort key "%s". Using the default \''}; {'id': '35', 'type': 'string', 'children': [], 'value': '\'"ram" instead.\''}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '37', 'type': 'return_statement', 'children': ['38']}; {'id': '38', 'type': 'call', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '40', 'type': 'argument_list', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'flavor'}; {'id': '42', 'type': 'string', 'children': [], 'value': "'ram'"}; {'id': '43', 'type': 'try_statement', 'children': ['44', '143']}; {'id': '44', 'type': 'block', 'children': ['45', '54', '64', '74', '98', '141']}; {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'flavor_sort'}; {'id': '48', 'type': 'call', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '50', 'type': 'argument_list', 'children': ['51', '52', '53']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'settings'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'CREATE_INSTANCE_FLAVOR_SORT'"}; {'id': '53', 'type': 'dictionary', 'children': []}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}; {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'flavor_sort'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '61', 'type': 'argument_list', 'children': ['62', '63']}; {'id': '62', 'type': 'string', 'children': [], 'value': "'key'"}; {'id': '63', 'type': 'string', 'children': [], 'value': "'ram'"}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}; {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'rev'}; {'id': '67', 'type': 'call', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'flavor_sort'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '71', 'type': 'argument_list', 'children': ['72', '73']}; {'id': '72', 'type': 'string', 'children': [], 'value': "'reverse'"}; {'id': '73', 'type': 'False', 'children': []}; {'id': '74', 'type': 'if_statement', 'children': ['75', '80', '92']}; {'id': '75', 'type': 'not_operator', 'children': ['76']}; {'id': '76', 'type': 'call', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'callable'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '80', 'type': 'block', 'children': ['81']}; {'id': '81', 'type': 'function_definition', 'children': ['82', '83', '85']}; {'id': '82', 'type': 'function_name', 'children': [], 'value': 'key'}; {'id': '83', 'type': 'parameters', 'children': ['84']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'flavor'}; {'id': '85', 'type': 'block', 'children': ['86']}; {'id': '86', 'type': 'return_statement', 'children': ['87']}; {'id': '87', 'type': 'call', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'get_key'}; {'id': '89', 'type': 'argument_list', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'flavor'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '92', 'type': 'else_clause', 'children': ['93']}; {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '98', 'type': 'if_statement', 'children': ['99', '100', '126']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'with_menu_label'}; {'id': '100', 'type': 'block', 'children': ['101']}; {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'flavor_list'}; {'id': '104', 'type': 'list_comprehension', 'children': ['105', '114']}; {'id': '105', 'type': 'tuple', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'flavor'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '109', 'type': 'binary_operator', 'children': ['110', '111'], 'value': '%'}; {'id': '110', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'flavor'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '114', 'type': 'for_in_clause', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'flavor'}; {'id': '116', 'type': 'call', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '118', 'type': 'argument_list', 'children': ['119', '120', '123']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'flavors'}; {'id': '120', 'type': 'keyword_argument', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '123', 'type': 'keyword_argument', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'rev'}; {'id': '126', 'type': 'else_clause', 'children': ['127']}; {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}; {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'flavor_list'}; {'id': '131', 'type': 'call', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '133', 'type': 'argument_list', 'children': ['134', '135', '138']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'flavors'}; {'id': '135', 'type': 'keyword_argument', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '138', 'type': 'keyword_argument', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'rev'}; {'id': '141', 'type': 'return_statement', 'children': ['142']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'flavor_list'}; {'id': '143', 'type': 'except_clause', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '145', 'type': 'block', 'children': ['146', '157']}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'exceptions'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'handle'}; {'id': '151', 'type': 'argument_list', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '153', 'type': 'call', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'string', 'children': [], 'value': "'Unable to sort instance flavors.'"}; {'id': '157', 'type': 'return_statement', 'children': ['158']}; {'id': '158', 'type': 'list', 'children': [], 'value': '[]'} | def sort_flavor_list(request, flavors, with_menu_label=True):
def get_key(flavor, sort_key):
try:
return getattr(flavor, sort_key)
except AttributeError:
LOG.warning('Could not find sort key "%s". Using the default '
'"ram" instead.', sort_key)
return getattr(flavor, 'ram')
try:
flavor_sort = getattr(settings, 'CREATE_INSTANCE_FLAVOR_SORT', {})
sort_key = flavor_sort.get('key', 'ram')
rev = flavor_sort.get('reverse', False)
if not callable(sort_key):
def key(flavor):
return get_key(flavor, sort_key)
else:
key = sort_key
if with_menu_label:
flavor_list = [(flavor.id, '%s' % flavor.name)
for flavor in sorted(flavors, key=key, reverse=rev)]
else:
flavor_list = sorted(flavors, key=key, reverse=rev)
return flavor_list
except Exception:
exceptions.handle(request,
_('Unable to sort instance flavors.'))
return [] |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '25']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'image_list_detailed'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20', '23']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'sort_dir'}; {'id': '10', 'type': 'string', 'children': [], 'value': "'desc'"}; {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '13', 'type': 'string', 'children': [], 'value': "'created_at'"}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '16', 'type': 'None', 'children': []}; {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'paginate'}; {'id': '19', 'type': 'False', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'reversed_order'}; {'id': '22', 'type': 'False', 'children': []}; {'id': '23', 'type': 'dictionary_splat_pattern', 'children': ['24']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '25', 'type': 'block', 'children': ['26', '35', '44', '59', '66', '75', '84', '90', '113', '134', '138', '142', '249', '253', '267']}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '31', 'type': 'argument_list', 'children': ['32', '33', '34']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'settings'}; {'id': '33', 'type': 'string', 'children': [], 'value': "'API_RESULT_LIMIT'"}; {'id': '34', 'type': 'integer', 'children': [], 'value': '1000'}; {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '38', 'type': 'call', 'children': ['39', '42']}; {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'get_page_size'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '44', 'type': 'if_statement', 'children': ['45', '46', '53']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'paginate'}; {'id': '46', 'type': 'block', 'children': ['47']}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'request_size'}; {'id': '50', 'type': 'binary_operator', 'children': ['51', '52'], 'value': '+'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '52', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '53', 'type': 'else_clause', 'children': ['54']}; {'id': '54', 'type': 'block', 'children': ['55']}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'request_size'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'call', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': '_normalize_list_input'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '64', 'type': 'dictionary_splat', 'children': ['65']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '69', 'type': 'dictionary', 'children': ['70']}; {'id': '70', 'type': 'pair', 'children': ['71', '72']}; {'id': '71', 'type': 'string', 'children': [], 'value': "'filters'"}; {'id': '72', 'type': 'boolean_operator', 'children': ['73', '74'], 'value': 'or'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '74', 'type': 'dictionary', 'children': []}; {'id': '75', 'type': 'if_statement', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '77', 'type': 'block', 'children': ['78']}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}; {'id': '79', 'type': 'assignment', 'children': ['80', '83']}; {'id': '80', 'type': 'subscript', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '82', 'type': 'string', 'children': [], 'value': "'marker'"}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}; {'id': '85', 'type': 'assignment', 'children': ['86', '89']}; {'id': '86', 'type': 'subscript', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '88', 'type': 'string', 'children': [], 'value': "'sort_key'"}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '90', 'type': 'if_statement', 'children': ['91', '93', '100']}; {'id': '91', 'type': 'not_operator', 'children': ['92']}; 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{'id': '108', 'type': 'string', 'children': [], 'value': "'desc'"}; {'id': '109', 'type': 'comparison_operator', 'children': ['110', '111'], 'value': '=='}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'sort_dir'}; {'id': '111', 'type': 'string', 'children': [], 'value': "'asc'"}; {'id': '112', 'type': 'string', 'children': [], 'value': "'asc'"}; {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'images_iter'}; {'id': '116', 'type': 'call', 'children': ['117', '125']}; {'id': '117', 'type': 'attribute', 'children': ['118', '124']}; {'id': '118', 'type': 'attribute', 'children': ['119', '123']}; {'id': '119', 'type': 'call', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'glanceclient'}; {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'request'}; 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{'id': '153', 'type': 'identifier', 'children': [], 'value': 'itertools'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'islice'}; {'id': '155', 'type': 'argument_list', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'images_iter'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'request_size'}; {'id': '158', 'type': 'if_statement', 'children': ['159', '165', '187', '198']}; {'id': '159', 'type': 'comparison_operator', 'children': ['160', '164'], 'value': '>'}; {'id': '160', 'type': 'call', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'images'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '165', 'type': 'block', 'children': ['166', '174', '178']}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}; {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'images'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'unary_operator', 'children': ['173'], 'value': '-'}; {'id': '173', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}; {'id': '175', 'type': 'assignment', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'has_more_data'}; {'id': '177', 'type': 'True', 'children': []}; {'id': '178', 'type': 'if_statement', 'children': ['179', '182']}; {'id': '179', 'type': 'comparison_operator', 'children': ['180', '181'], 'value': 'is'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '181', 'type': 'None', 'children': []}; {'id': '182', 'type': 'block', 'children': ['183']}; 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{'id': '229', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '231', 'type': 'string', 'children': [], 'value': "''"}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'lower'}; {'id': '233', 'type': 'argument_list', 'children': []}; {'id': '234', 'type': 'keyword_argument', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '236', 'type': '()', 'children': ['237']}; {'id': '237', 'type': 'comparison_operator', 'children': ['238', '239'], 'value': '=='}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'sort_dir'}; {'id': '239', 'type': 'string', 'children': [], 'value': "'desc'"}; {'id': '240', 'type': 'else_clause', 'children': ['241']}; {'id': '241', 'type': 'block', 'children': ['242']}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}; {'id': '243', 'type': 'assignment', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'images'}; {'id': '245', 'type': 'call', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'images_iter'}; {'id': '249', 'type': 'expression_statement', 'children': ['250']}; {'id': '250', 'type': 'assignment', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'wrapped_images'}; {'id': '252', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '253', 'type': 'for_statement', 'children': ['254', '255', '256']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'images'}; {'id': '256', 'type': 'block', 'children': ['257']}; {'id': '257', 'type': 'expression_statement', 'children': ['258']}; {'id': '258', 'type': 'call', 'children': ['259', '262']}; {'id': '259', 'type': 'attribute', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'wrapped_images'}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '262', 'type': 'argument_list', 'children': ['263']}; {'id': '263', 'type': 'call', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'Image'}; {'id': '265', 'type': 'argument_list', 'children': ['266']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '267', 'type': 'return_statement', 'children': ['268']}; {'id': '268', 'type': 'expression_list', 'children': ['269', '270', '271']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'wrapped_images'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'has_more_data'}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'has_prev_data'} | def image_list_detailed(request, marker=None, sort_dir='desc',
sort_key='created_at', filters=None, paginate=False,
reversed_order=False, **kwargs):
limit = getattr(settings, 'API_RESULT_LIMIT', 1000)
page_size = utils.get_page_size(request)
if paginate:
request_size = page_size + 1
else:
request_size = limit
_normalize_list_input(filters, **kwargs)
kwargs = {'filters': filters or {}}
if marker:
kwargs['marker'] = marker
kwargs['sort_key'] = sort_key
if not reversed_order:
kwargs['sort_dir'] = sort_dir
else:
kwargs['sort_dir'] = 'desc' if sort_dir == 'asc' else 'asc'
images_iter = glanceclient(request).images.list(page_size=request_size,
limit=limit,
**kwargs)
has_prev_data = False
has_more_data = False
if paginate:
images = list(itertools.islice(images_iter, request_size))
if len(images) > page_size:
images.pop(-1)
has_more_data = True
if marker is not None:
has_prev_data = True
elif reversed_order and marker is not None:
has_more_data = True
elif marker is not None:
has_prev_data = True
if reversed_order:
images = sorted(images, key=lambda image:
(getattr(image, sort_key) or '').lower(),
reverse=(sort_dir == 'desc'))
else:
images = list(images_iter)
wrapped_images = []
for image in images:
wrapped_images.append(Image(image))
return wrapped_images, has_more_data, has_prev_data |
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{'id': '47', 'type': 'argument_list', 'children': ['48', '49', '50']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'settings'}; {'id': '49', 'type': 'string', 'children': [], 'value': "'API_RESULT_LIMIT'"}; {'id': '50', 'type': 'integer', 'children': [], 'value': '1000'}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'get_page_size'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '60', 'type': 'if_statement', 'children': ['61', '62', '69']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'paginate'}; {'id': '62', 'type': 'block', 'children': ['63']}; {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'request_size'}; {'id': '66', 'type': 'binary_operator', 'children': ['67', '68'], 'value': '+'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '68', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '69', 'type': 'else_clause', 'children': ['70']}; {'id': '70', 'type': 'block', 'children': ['71']}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'request_size'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '78', 'type': 'dictionary', 'children': ['79']}; {'id': '79', 'type': 'pair', 'children': ['80', '81']}; {'id': '80', 'type': 'string', 'children': [], 'value': "'filters'"}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '82', 'type': 'if_statement', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '84', 'type': 'block', 'children': ['85']}; {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '90']}; {'id': '87', 'type': 'subscript', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '89', 'type': 'string', 'children': [], 'value': "'marker'"}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '96']}; {'id': '93', 'type': 'subscript', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '95', 'type': 'string', 'children': [], 'value': "'sort_dir'"}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'sort_dir'}; {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '102']}; {'id': '99', 'type': 'subscript', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '101', 'type': 'string', 'children': [], 'value': "'sort_key'"}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'namespaces_iter'}; {'id': '106', 'type': 'call', 'children': ['107', '116']}; {'id': '107', 'type': 'attribute', 'children': ['108', '115']}; {'id': '108', 'type': 'attribute', 'children': ['109', '114']}; {'id': '109', 'type': 'call', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'glanceclient'}; {'id': '111', 'type': 'argument_list', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '113', 'type': 'string', 'children': [], 'value': "'2'"}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'metadefs_namespace'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '116', 'type': 'argument_list', 'children': ['117', '120', '123']}; {'id': '117', 'type': 'keyword_argument', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'request_size'}; {'id': '120', 'type': 'keyword_argument', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '123', 'type': 'dictionary_splat', 'children': ['124']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'resource_types'}; {'id': '128', 'type': 'call', 'children': ['129', '132']}; {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '132', 'type': 'argument_list', 'children': ['133']}; {'id': '133', 'type': 'string', 'children': [], 'value': "'resource_types'"}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'properties_target'}; {'id': '137', 'type': 'call', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '141', 'type': 'argument_list', 'children': ['142']}; {'id': '142', 'type': 'string', 'children': [], 'value': "'properties_target'"}; {'id': '143', 'type': 'if_statement', 'children': ['144', '147']}; {'id': '144', 'type': 'boolean_operator', 'children': ['145', '146'], 'value': 'and'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'resource_types'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'properties_target'}; {'id': '147', 'type': 'block', 'children': ['148']}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}; {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'namespaces_iter'}; {'id': '151', 'type': 'call', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'filter_properties_target'}; {'id': '153', 'type': 'argument_list', 'children': ['154', '155', '156']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'namespaces_iter'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'resource_types'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'properties_target'}; {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'has_prev_data'}; {'id': '160', 'type': 'False', 'children': []}; {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'assignment', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'has_more_data'}; {'id': '164', 'type': 'False', 'children': []}; {'id': '165', 'type': 'if_statement', 'children': ['166', '167', '232']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'paginate'}; {'id': '167', 'type': 'block', 'children': ['168', '181']}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}; {'id': '169', 'type': 'assignment', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'namespaces'}; {'id': '171', 'type': 'call', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '173', 'type': 'argument_list', 'children': ['174']}; {'id': '174', 'type': 'call', 'children': ['175', '178']}; {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'itertools'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'islice'}; {'id': '178', 'type': 'argument_list', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'namespaces_iter'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'request_size'}; {'id': '181', 'type': 'if_statement', 'children': ['182', '188', '210', '223']}; {'id': '182', 'type': 'comparison_operator', 'children': ['183', '187'], 'value': '>'}; {'id': '183', 'type': 'call', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '185', 'type': 'argument_list', 'children': ['186']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'namespaces'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '188', 'type': 'block', 'children': ['189', '197', '201']}; {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'call', 'children': ['191', '194']}; {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'namespaces'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '194', 'type': 'argument_list', 'children': ['195']}; {'id': '195', 'type': 'unary_operator', 'children': ['196'], 'value': '-'}; {'id': '196', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'assignment', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'has_more_data'}; {'id': '200', 'type': 'True', 'children': []}; {'id': '201', 'type': 'if_statement', 'children': ['202', '205']}; {'id': '202', 'type': 'comparison_operator', 'children': ['203', '204'], 'value': 'is'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '204', 'type': 'None', 'children': []}; {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}; {'id': '207', 'type': 'assignment', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'has_prev_data'}; {'id': '209', 'type': 'True', 'children': []}; {'id': '210', 'type': 'elif_clause', 'children': ['211', '218']}; {'id': '211', 'type': 'boolean_operator', 'children': ['212', '215'], 'value': 'and'}; {'id': '212', 'type': 'comparison_operator', 'children': ['213', '214'], 'value': '=='}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'sort_dir'}; {'id': '214', 'type': 'string', 'children': [], 'value': "'desc'"}; {'id': '215', 'type': 'comparison_operator', 'children': ['216', '217'], 'value': 'is'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '217', 'type': 'None', 'children': []}; {'id': '218', 'type': 'block', 'children': ['219']}; {'id': '219', 'type': 'expression_statement', 'children': ['220']}; {'id': '220', 'type': 'assignment', 'children': ['221', '222']}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'has_more_data'}; {'id': '222', 'type': 'True', 'children': []}; {'id': '223', 'type': 'elif_clause', 'children': ['224', '227']}; {'id': '224', 'type': 'comparison_operator', 'children': ['225', '226'], 'value': 'is'}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '226', 'type': 'None', 'children': []}; {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}; {'id': '229', 'type': 'assignment', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'has_prev_data'}; {'id': '231', 'type': 'True', 'children': []}; {'id': '232', 'type': 'else_clause', 'children': ['233']}; {'id': '233', 'type': 'block', 'children': ['234']}; {'id': '234', 'type': 'expression_statement', 'children': ['235']}; {'id': '235', 'type': 'assignment', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'namespaces'}; {'id': '237', 'type': 'call', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '239', 'type': 'argument_list', 'children': ['240']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'namespaces_iter'}; {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'assignment', 'children': ['243', '244']}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'namespaces'}; {'id': '244', 'type': 'list_comprehension', 'children': ['245', '249']}; {'id': '245', 'type': 'call', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'Namespace'}; {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'namespace'}; {'id': '249', 'type': 'for_in_clause', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'namespace'}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'namespaces'}; {'id': '252', 'type': 'return_statement', 'children': ['253']}; {'id': '253', 'type': 'expression_list', 'children': ['254', '255', '256']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'namespaces'}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'has_more_data'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'has_prev_data'} | def metadefs_namespace_list(request,
filters=None,
sort_dir='asc',
sort_key='namespace',
marker=None,
paginate=False):
if get_version() < 2:
return [], False, False
if filters is None:
filters = {}
limit = getattr(settings, 'API_RESULT_LIMIT', 1000)
page_size = utils.get_page_size(request)
if paginate:
request_size = page_size + 1
else:
request_size = limit
kwargs = {'filters': filters}
if marker:
kwargs['marker'] = marker
kwargs['sort_dir'] = sort_dir
kwargs['sort_key'] = sort_key
namespaces_iter = glanceclient(request, '2').metadefs_namespace.list(
page_size=request_size, limit=limit, **kwargs)
resource_types = filters.get('resource_types')
properties_target = filters.get('properties_target')
if resource_types and properties_target:
namespaces_iter = filter_properties_target(namespaces_iter,
resource_types,
properties_target)
has_prev_data = False
has_more_data = False
if paginate:
namespaces = list(itertools.islice(namespaces_iter, request_size))
if len(namespaces) > page_size:
namespaces.pop(-1)
has_more_data = True
if marker is not None:
has_prev_data = True
elif sort_dir == 'desc' and marker is not None:
has_more_data = True
elif marker is not None:
has_prev_data = True
else:
namespaces = list(namespaces_iter)
namespaces = [Namespace(namespace) for namespace in namespaces]
return namespaces, has_more_data, has_prev_data |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_js_files'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'js_files'}; {'id': '5', 'type': 'block', 'children': ['6', '21', '36', '51', '84', '90']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'modules'}; {'id': '9', 'type': 'list_comprehension', 'children': ['10', '11', '14']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '11', 'type': 'for_in_clause', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'js_files'}; {'id': '14', 'type': 'if_clause', 'children': ['15']}; {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'MODULE_EXT'}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'mocks'}; {'id': '24', 'type': 'list_comprehension', 'children': ['25', '26', '29']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '26', 'type': 'for_in_clause', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'js_files'}; {'id': '29', 'type': 'if_clause', 'children': ['30']}; {'id': '30', 'type': 'call', 'children': ['31', '34']}; {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'MOCK_EXT'}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}; {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'specs'}; {'id': '39', 'type': 'list_comprehension', 'children': ['40', '41', '44']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '41', 'type': 'for_in_clause', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'js_files'}; {'id': '44', 'type': 'if_clause', 'children': ['45']}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'SPEC_EXT'}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'other_sources'}; {'id': '54', 'type': 'list_comprehension', 'children': ['55', '56', '59']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '56', 'type': 'for_in_clause', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'js_files'}; {'id': '59', 'type': 'if_clause', 'children': ['60']}; {'id': '60', 'type': '()', 'children': ['61']}; {'id': '61', 'type': 'boolean_operator', 'children': ['62', '77'], 'value': 'and'}; {'id': '62', 'type': 'boolean_operator', 'children': ['63', '70'], 'value': 'and'}; {'id': '63', 'type': 'not_operator', 'children': ['64']}; {'id': '64', 'type': 'call', 'children': ['65', '68']}; {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'MODULE_EXT'}; {'id': '70', 'type': 'not_operator', 'children': ['71']}; {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'MOCK_EXT'}; {'id': '77', 'type': 'not_operator', 'children': ['78']}; {'id': '78', 'type': 'call', 'children': ['79', '82']}; {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'SPEC_EXT'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}; {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'sources'}; {'id': '87', 'type': 'binary_operator', 'children': ['88', '89'], 'value': '+'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'modules'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'other_sources'}; {'id': '90', 'type': 'return_statement', 'children': ['91']}; {'id': '91', 'type': 'expression_list', 'children': ['92', '93', '94']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'sources'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'mocks'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'specs'} | def sort_js_files(js_files):
modules = [f for f in js_files if f.endswith(MODULE_EXT)]
mocks = [f for f in js_files if f.endswith(MOCK_EXT)]
specs = [f for f in js_files if f.endswith(SPEC_EXT)]
other_sources = [f for f in js_files
if (not f.endswith(MODULE_EXT) and
not f.endswith(MOCK_EXT) and
not f.endswith(SPEC_EXT))]
sources = modules + other_sources
return sources, mocks, specs |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_slice_mostly_sorted'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'rest'}; {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'ind'}; {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'block', 'children': ['11', '28', '46', '50', '70', '80', '97', '131', '160', '177']}; {'id': '11', 'type': 'if_statement', 'children': ['12', '15']}; {'id': '12', 'type': 'comparison_operator', 'children': ['13', '14'], 'value': 'is'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'ind'}; {'id': '14', 'type': 'None', 'children': []}; {'id': '15', 'type': 'block', 'children': ['16']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'ind'}; {'id': '19', 'type': 'call', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'arange'}; {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'call', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}; {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '31', 'type': 'call', 'children': ['32', '35']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'argsort'}; {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'call', 'children': ['37', '40']}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'concatenate'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}; {'id': '41', 'type': 'list', 'children': ['42', '43'], 'value': '[keep, ind[rest]]'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '43', 'type': 'subscript', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'ind'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'rest'}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'slices'}; {'id': '49', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '50', 'type': 'if_statement', 'children': ['51', '56']}; {'id': '51', 'type': 'comparison_operator', 'children': ['52', '55'], 'value': '>'}; {'id': '52', 'type': 'subscript', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '54', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '55', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '56', 'type': 'block', 'children': ['57']}; {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'call', 'children': ['59', '62']}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'slices'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}; {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'slice'}; {'id': '65', 'type': 'argument_list', 'children': ['66', '67']}; {'id': '66', 'type': 'None', 'children': []}; {'id': '67', 'type': 'subscript', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '69', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}; {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'slices'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'list', 'children': ['77'], 'value': '[keep[0]]'}; {'id': '77', 'type': 'subscript', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '79', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'windows'}; {'id': '83', 'type': 'call', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '85', 'type': 'argument_list', 'children': ['86', '92']}; {'id': '86', 'type': 'subscript', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '88', 'type': 'slice', 'children': ['89', '90']}; {'id': '89', 'type': 'colon', 'children': []}; {'id': '90', 'type': 'unary_operator', 'children': ['91'], 'value': '-'}; {'id': '91', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '92', 'type': 'subscript', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '94', 'type': 'slice', 'children': ['95', '96']}; {'id': '95', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '96', 'type': 'colon', 'children': []}; {'id': '97', 'type': 'for_statement', 'children': ['98', '101', '102']}; {'id': '98', 'type': 'pattern_list', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'l'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'windows'}; {'id': '102', 'type': 'block', 'children': ['103', '123']}; {'id': '103', 'type': 'if_statement', 'children': ['104', '109']}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '106'], 'value': '>'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '106', 'type': 'binary_operator', 'children': ['107', '108'], 'value': '+'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'l'}; {'id': '108', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}; {'id': '111', 'type': 'call', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'slices'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'call', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'slice'}; {'id': '118', 'type': 'argument_list', 'children': ['119', '122']}; {'id': '119', 'type': 'binary_operator', 'children': ['120', '121'], 'value': '+'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'l'}; {'id': '121', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '128']}; {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'slices'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}; {'id': '129', 'type': 'list', 'children': ['130'], 'value': '[r]'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '131', 'type': 'if_statement', 'children': ['132', '143']}; {'id': '132', 'type': 'comparison_operator', 'children': ['133', '137'], 'value': '<'}; {'id': '133', 'type': 'subscript', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '135', 'type': 'unary_operator', 'children': ['136'], 'value': '-'}; {'id': '136', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '137', 'type': 'binary_operator', 'children': ['138', '142'], 'value': '-'}; {'id': '138', 'type': 'call', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '142', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '143', 'type': 'block', 'children': ['144']}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}; {'id': '145', 'type': 'call', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'slices'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '149', 'type': 'argument_list', 'children': ['150']}; {'id': '150', 'type': 'call', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'slice'}; {'id': '152', 'type': 'argument_list', 'children': ['153', '159']}; {'id': '153', 'type': 'binary_operator', 'children': ['154', '158'], 'value': '+'}; {'id': '154', 'type': 'subscript', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '156', 'type': 'unary_operator', 'children': ['157'], 'value': '-'}; {'id': '157', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '158', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '159', 'type': 'None', 'children': []}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}; {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '163', 'type': 'call', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'da'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'concatenate'}; {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'list_comprehension', 'children': ['169', '174']}; {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '171', 'type': 'subscript', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'slice_'}; {'id': '174', 'type': 'for_in_clause', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'slice_'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'slices'}; {'id': '177', 'type': 'return_statement', 'children': ['178']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'result'} | def _slice_mostly_sorted(array, keep, rest, ind=None):
if ind is None:
ind = np.arange(len(array))
idx = np.argsort(np.concatenate([keep, ind[rest]]))
slices = []
if keep[0] > 0:
slices.append(slice(None, keep[0]))
slices.append([keep[0]])
windows = zip(keep[:-1], keep[1:])
for l, r in windows:
if r > l + 1:
slices.append(slice(l + 1, r))
slices.append([r])
if keep[-1] < len(array) - 1:
slices.append(slice(keep[-1] + 1, None))
result = da.concatenate([array[idx[slice_]] for slice_ in slices])
return result |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12', '24']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_servers_closest'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'typed_parameter', 'children': ['5', '6']}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'servers'}; {'id': '6', 'type': 'type', 'children': ['7']}; {'id': '7', 'type': 'generic_type', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'Sequence'}; {'id': '9', 'type': 'type_parameter', 'children': ['10']}; {'id': '10', 'type': 'type', 'children': ['11']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '12', 'type': 'type', 'children': ['13']}; {'id': '13', 'type': 'generic_type', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'Sequence'}; {'id': '15', 'type': 'type_parameter', 'children': ['16']}; {'id': '16', 'type': 'type', 'children': ['17']}; {'id': '17', 'type': 'generic_type', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'Tuple'}; {'id': '19', 'type': 'type_parameter', 'children': ['20', '22']}; {'id': '20', 'type': 'type', 'children': ['21']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '22', 'type': 'type', 'children': ['23']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '24', 'type': 'block', 'children': ['25', '50', '74', '84', '123', '133']}; {'id': '25', 'type': 'if_statement', 'children': ['26', '44']}; {'id': '26', 'type': 'not_operator', 'children': ['27']}; {'id': '27', 'type': 'call', 'children': ['28', '40']}; {'id': '28', 'type': 'attribute', 'children': ['29', '39']}; {'id': '29', 'type': 'set_comprehension', 'children': ['30', '36']}; {'id': '30', 'type': 'attribute', 'children': ['31', '35']}; {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'urlparse'}; {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'scheme'}; {'id': '36', 'type': 'for_in_clause', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'servers'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'issubset'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}; {'id': '41', 'type': 'set', 'children': ['42', '43']}; {'id': '42', 'type': 'string', 'children': [], 'value': "'http'"}; {'id': '43', 'type': 'string', 'children': [], 'value': "'https'"}; {'id': '44', 'type': 'block', 'children': ['45']}; {'id': '45', 'type': 'raise_statement', 'children': ['46']}; {'id': '46', 'type': 'call', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'TransportError'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}; {'id': '49', 'type': 'string', 'children': [], 'value': "'Invalid server urls'"}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}; {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'get_rtt_jobs'}; {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '55', 'type': 'generator_expression', 'children': ['56', '71']}; {'id': '56', 'type': 'call', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'gevent'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'spawn'}; {'id': '60', 'type': 'argument_list', 'children': ['61', '70']}; {'id': '61', 'type': 'lambda', 'children': ['62', '64']}; {'id': '62', 'type': 'lambda_parameters', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '64', 'type': 'tuple', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '66', 'type': 'call', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'get_http_rtt'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'server_url'}; {'id': '71', 'type': 'for_in_clause', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'server_url'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'servers'}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}; {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'gevent'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'joinall'}; {'id': '79', 'type': 'argument_list', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'get_rtt_jobs'}; {'id': '81', 'type': 'keyword_argument', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'raise_error'}; {'id': '83', 'type': 'False', 'children': []}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}; {'id': '85', 'type': 'assignment', 'children': ['86', '87', '99']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'sorted_servers'}; {'id': '87', 'type': 'type', 'children': ['88']}; {'id': '88', 'type': 'generic_type', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'List'}; {'id': '90', 'type': 'type_parameter', 'children': ['91']}; {'id': '91', 'type': 'type', 'children': ['92']}; {'id': '92', 'type': 'generic_type', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'Tuple'}; {'id': '94', 'type': 'type_parameter', 'children': ['95', '97']}; {'id': '95', 'type': 'type', 'children': ['96']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '97', 'type': 'type', 'children': ['98']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '101', 'type': 'argument_list', 'children': ['102', '117']}; {'id': '102', 'type': 'generator_expression', 'children': ['103', '106', '109']}; {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'job'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '106', 'type': 'for_in_clause', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'job'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'get_rtt_jobs'}; {'id': '109', 'type': 'if_clause', 'children': ['110']}; {'id': '110', 'type': 'comparison_operator', 'children': ['111', '116'], 'value': 'is'}; {'id': '111', 'type': 'subscript', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'job'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '115', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '116', 'type': 'None', 'children': []}; {'id': '117', 'type': 'keyword_argument', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '119', 'type': 'call', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'itemgetter'}; {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '128']}; {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '128', 'type': 'argument_list', 'children': ['129', '130']}; {'id': '129', 'type': 'string', 'children': [], 'value': "'Matrix homeserver RTT times'"}; {'id': '130', 'type': 'keyword_argument', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'rtt_times'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'sorted_servers'}; {'id': '133', 'type': 'return_statement', 'children': ['134']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'sorted_servers'} | def sort_servers_closest(servers: Sequence[str]) -> Sequence[Tuple[str, float]]:
if not {urlparse(url).scheme for url in servers}.issubset({'http', 'https'}):
raise TransportError('Invalid server urls')
get_rtt_jobs = set(
gevent.spawn(lambda url: (url, get_http_rtt(url)), server_url)
for server_url
in servers
)
gevent.joinall(get_rtt_jobs, raise_error=False)
sorted_servers: List[Tuple[str, float]] = sorted(
(job.value for job in get_rtt_jobs if job.value[1] is not None),
key=itemgetter(1),
)
log.debug('Matrix homeserver RTT times', rtt_times=sorted_servers)
return sorted_servers |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_runs_by_id'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'config_id'}; {'id': '6', 'type': 'block', 'children': ['7', '15', '19', '108', '122']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '10', 'type': 'subscript', 'children': ['11', '14']}; {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'config_id'}; {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'runs'}; {'id': '18', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '19', 'type': 'for_statement', 'children': ['20', '21', '28']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '21', 'type': 'call', 'children': ['22', '27']}; {'id': '22', 'type': 'attribute', 'children': ['23', '26']}; {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '27', 'type': 'argument_list', 'children': []}; {'id': '28', 'type': 'block', 'children': ['29']}; {'id': '29', 'type': 'try_statement', 'children': ['30', '105']}; {'id': '30', 'type': 'block', 'children': ['31', '43', '98']}; {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'err_logs'}; {'id': '34', 'type': 'call', 'children': ['35', '40']}; {'id': '35', 'type': 'attribute', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'exceptions'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '40', 'type': 'argument_list', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '42', 'type': 'None', 'children': []}; {'id': '43', 'type': 'if_statement', 'children': ['44', '51', '68']}; {'id': '44', 'type': 'comparison_operator', 'children': ['45', '50'], 'value': 'is'}; {'id': '45', 'type': 'subscript', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '50', 'type': 'None', 'children': []}; {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}; {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '55', 'type': 'call', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'Run'}; {'id': '57', 'type': 'argument_list', 'children': ['58', '59', '60', '61', '62', '67']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'config_id'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '60', 'type': 'None', 'children': []}; {'id': '61', 'type': 'None', 'children': []}; {'id': '62', 'type': 'subscript', 'children': ['63', '66']}; {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'time_stamps'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'err_logs'}; {'id': '68', 'type': 'else_clause', 'children': ['69']}; {'id': '69', 'type': 'block', 'children': ['70']}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}; {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '73', 'type': 'call', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'Run'}; {'id': '75', 'type': 'argument_list', 'children': ['76', '77', '78', '85', '92', '97']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'config_id'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '78', 'type': 'subscript', 'children': ['79', '84']}; {'id': '79', 'type': 'subscript', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '84', 'type': 'string', 'children': [], 'value': "'loss'"}; {'id': '85', 'type': 'subscript', 'children': ['86', '91']}; {'id': '86', 'type': 'subscript', 'children': ['87', '90']}; {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '91', 'type': 'string', 'children': [], 'value': "'info'"}; {'id': '92', 'type': 'subscript', 'children': ['93', '96']}; {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'time_stamps'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'err_logs'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}; {'id': '99', 'type': 'call', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'runs'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '105', 'type': 'except_clause', 'children': ['106']}; {'id': '106', 'type': 'block', 'children': ['107']}; {'id': '107', 'type': 'raise_statement', 'children': []}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}; {'id': '109', 'type': 'call', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'runs'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '113', 'type': 'argument_list', 'children': ['114']}; {'id': '114', 'type': 'keyword_argument', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '116', 'type': 'lambda', 'children': ['117', '119']}; {'id': '117', 'type': 'lambda_parameters', 'children': ['118']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'budget'}; {'id': '122', 'type': 'return_statement', 'children': ['123']}; {'id': '123', 'type': '()', 'children': ['124']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'runs'} | def get_runs_by_id(self, config_id):
d = self.data[config_id]
runs = []
for b in d.results.keys():
try:
err_logs = d.exceptions.get(b, None)
if d.results[b] is None:
r = Run(config_id, b, None, None , d.time_stamps[b], err_logs)
else:
r = Run(config_id, b, d.results[b]['loss'], d.results[b]['info'] , d.time_stamps[b], err_logs)
runs.append(r)
except:
raise
runs.sort(key=lambda r: r.budget)
return(runs) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9', '15']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'spell'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'typed_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'word'}; {'id': '7', 'type': 'type', 'children': ['8']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '9', 'type': 'type', 'children': ['10']}; {'id': '10', 'type': 'generic_type', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'List'}; {'id': '12', 'type': 'type_parameter', 'children': ['13']}; {'id': '13', 'type': 'type', 'children': ['14']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '15', 'type': 'block', 'children': ['16', '22', '56', '70']}; {'id': '16', 'type': 'if_statement', 'children': ['17', '19']}; {'id': '17', 'type': 'not_operator', 'children': ['18']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'word'}; {'id': '19', 'type': 'block', 'children': ['20']}; {'id': '20', 'type': 'return_statement', 'children': ['21']}; {'id': '21', 'type': 'string', 'children': [], 'value': '""'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'candidates'}; {'id': '25', 'type': '()', 'children': ['26']}; {'id': '26', 'type': 'boolean_operator', 'children': ['27', '54'], 'value': 'or'}; {'id': '27', 'type': 'boolean_operator', 'children': ['28', '45'], 'value': 'or'}; {'id': '28', 'type': 'boolean_operator', 'children': ['29', '36'], 'value': 'or'}; {'id': '29', 'type': 'call', 'children': ['30', '33']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'known'}; {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'list', 'children': ['35'], 'value': '[word]'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'word'}; {'id': '36', 'type': 'call', 'children': ['37', '40']}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'known'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}; {'id': '41', 'type': 'call', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': '_edits1'}; {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'word'}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'known'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': '_edits2'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'word'}; {'id': '54', 'type': 'list', 'children': ['55'], 'value': '[word]'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'word'}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}; {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'candidates'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '61', 'type': 'argument_list', 'children': ['62', '67']}; {'id': '62', 'type': 'keyword_argument', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'freq'}; {'id': '67', 'type': 'keyword_argument', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '69', 'type': 'True', 'children': []}; {'id': '70', 'type': 'return_statement', 'children': ['71']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'candidates'} | def spell(self, word: str) -> List[str]:
if not word:
return ""
candidates = (
self.known([word])
or self.known(_edits1(word))
or self.known(_edits2(word))
or [word]
)
candidates.sort(key=self.freq, reverse=True)
return candidates |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17', '19']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'rank'}; {'id': '3', 'type': 'parameters', 'children': ['4', '12']}; {'id': '4', 'type': 'typed_parameter', 'children': ['5', '6']}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'words'}; {'id': '6', 'type': 'type', 'children': ['7']}; {'id': '7', 'type': 'generic_type', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'List'}; {'id': '9', 'type': 'type_parameter', 'children': ['10']}; {'id': '10', 'type': 'type', 'children': ['11']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '12', 'type': 'typed_default_parameter', 'children': ['13', '14', '16']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'exclude_stopwords'}; {'id': '14', 'type': 'type', 'children': ['15']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'bool'}; {'id': '16', 'type': 'False', 'children': []}; {'id': '17', 'type': 'type', 'children': ['18']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'Counter'}; {'id': '19', 'type': 'block', 'children': ['20', '26', '41']}; {'id': '20', 'type': 'if_statement', 'children': ['21', '23']}; {'id': '21', 'type': 'not_operator', 'children': ['22']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'words'}; {'id': '23', 'type': 'block', 'children': ['24']}; {'id': '24', 'type': 'return_statement', 'children': ['25']}; {'id': '25', 'type': 'None', 'children': []}; {'id': '26', 'type': 'if_statement', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'exclude_stopwords'}; {'id': '28', 'type': 'block', 'children': ['29']}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'words'}; {'id': '32', 'type': 'list_comprehension', 'children': ['33', '34', '37']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'word'}; {'id': '34', 'type': 'for_in_clause', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'word'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'words'}; {'id': '37', 'type': 'if_clause', 'children': ['38']}; {'id': '38', 'type': 'comparison_operator', 'children': ['39', '40'], 'value': 'not'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'word'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': '_STOPWORDS'}; {'id': '41', 'type': 'return_statement', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'Counter'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'words'} | def rank(words: List[str], exclude_stopwords: bool = False) -> Counter:
if not words:
return None
if exclude_stopwords:
words = [word for word in words if word not in _STOPWORDS]
return Counter(words) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '16']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'iter'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '7', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'pagesize'}; {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'dictionary_splat_pattern', 'children': ['15']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '16', 'type': 'block', 'children': ['17', '25', '36', '40']}; {'id': '17', 'type': 'assert_statement', 'children': ['18']}; {'id': '18', 'type': 'boolean_operator', 'children': ['19', '22'], 'value': 'or'}; {'id': '19', 'type': 'comparison_operator', 'children': ['20', '21'], 'value': 'is'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'pagesize'}; {'id': '21', 'type': 'None', 'children': []}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '24'], 'value': '>'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'pagesize'}; {'id': '24', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '25', 'type': 'if_statement', 'children': ['26', '29']}; {'id': '26', 'type': 'comparison_operator', 'children': ['27', '28'], 'value': 'is'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '28', 'type': 'None', 'children': []}; {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'null_count'}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}; {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'fetched'}; {'id': '39', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '40', 'type': 'while_statement', 'children': ['41', '50']}; {'id': '41', 'type': 'boolean_operator', 'children': ['42', '47'], 'value': 'or'}; {'id': '42', 'type': 'comparison_operator', 'children': ['43', '44'], 'value': '=='}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'null_count'}; {'id': '47', 'type': 'comparison_operator', 'children': ['48', '49'], 'value': '<'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'fetched'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '50', 'type': 'block', 'children': ['51', '69', '78', '85', '89', '96', '106', '110']}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '58', 'type': 'argument_list', 'children': ['59', '64', '67']}; {'id': '59', 'type': 'keyword_argument', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '61', 'type': 'boolean_operator', 'children': ['62', '63'], 'value': 'or'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'pagesize'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '64', 'type': 'keyword_argument', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '67', 'type': 'dictionary_splat', 'children': ['68']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '72', 'type': 'call', 'children': ['73', '76']}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': '_load_list'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}; {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'augmented_assignment', 'children': ['87', '88'], 'value': '+='}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'fetched'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '89', 'type': 'for_statement', 'children': ['90', '91', '92']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '92', 'type': 'block', 'children': ['93']}; {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'yield', 'children': ['95']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '96', 'type': 'if_statement', 'children': ['97', '104']}; {'id': '97', 'type': 'boolean_operator', 'children': ['98', '101'], 'value': 'or'}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '100'], 'value': 'is'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'pagesize'}; {'id': '100', 'type': 'None', 'children': []}; {'id': '101', 'type': 'comparison_operator', 'children': ['102', '103'], 'value': '<'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'pagesize'}; {'id': '104', 'type': 'block', 'children': ['105']}; {'id': '105', 'type': 'break_statement', 'children': []}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}; {'id': '107', 'type': 'augmented_assignment', 'children': ['108', '109'], 'value': '+='}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}; {'id': '111', 'type': 'call', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'logging'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '115', 'type': 'argument_list', 'children': ['116', '117', '118', '119', '120', '121']}; {'id': '116', 'type': 'string', 'children': [], 'value': '"pagesize=%d, fetched=%d, offset=%d, N=%d, kwargs=%s"'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'pagesize'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'fetched'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'kwargs'} | def iter(self, offset=0, count=None, pagesize=None, **kwargs):
assert pagesize is None or pagesize > 0
if count is None:
count = self.null_count
fetched = 0
while count == self.null_count or fetched < count:
response = self.get(count=pagesize or count, offset=offset, **kwargs)
items = self._load_list(response)
N = len(items)
fetched += N
for item in items:
yield item
if pagesize is None or N < pagesize:
break
offset += N
logging.debug("pagesize=%d, fetched=%d, offset=%d, N=%d, kwargs=%s", pagesize, fetched, offset, N, kwargs) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'list'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'dictionary_splat_pattern', 'children': ['9']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '10', 'type': 'block', 'children': ['11']}; {'id': '11', 'type': 'return_statement', 'children': ['12']}; {'id': '12', 'type': 'call', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '14', 'type': 'argument_list', 'children': ['15']}; {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'iter'}; {'id': '19', 'type': 'argument_list', 'children': ['20', '23']}; {'id': '20', 'type': 'keyword_argument', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '23', 'type': 'dictionary_splat', 'children': ['24']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'kwargs'} | def list(self, count=None, **kwargs):
return list(self.iter(count=count, **kwargs)) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'query'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '7', 'type': 'block', 'children': ['8']}; {'id': '8', 'type': 'return_statement', 'children': ['9']}; {'id': '9', 'type': 'call', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'loads'}; {'id': '13', 'type': 'argument_list', 'children': ['14']}; {'id': '14', 'type': 'call', 'children': ['15', '31']}; {'id': '15', 'type': 'attribute', 'children': ['16', '30']}; {'id': '16', 'type': 'call', 'children': ['17', '29']}; {'id': '17', 'type': 'attribute', 'children': ['18', '28']}; {'id': '18', 'type': 'attribute', 'children': ['19', '27']}; {'id': '19', 'type': 'call', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': '_get'}; {'id': '23', 'type': 'argument_list', 'children': ['24', '25']}; {'id': '24', 'type': 'string', 'children': [], 'value': "''"}; {'id': '25', 'type': 'dictionary_splat', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'body'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'read'}; {'id': '29', 'type': 'argument_list', 'children': []}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'decode'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'string', 'children': [], 'value': "'utf-8'"} | def query(self, **query):
return json.loads(self._get('', **query).body.read().decode('utf-8')) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '28']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'query'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20', '23', '26']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'area'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'date'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'raw'}; {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'area_relation'}; {'id': '16', 'type': 'string', 'children': [], 'value': "'Intersects'"}; {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'order_by'}; {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '22', 'type': 'None', 'children': []}; {'id': '23', 'type': 'default_parameter', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '25', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '26', 'type': 'dictionary_splat_pattern', 'children': ['27']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'keywords'}; {'id': '28', 'type': 'block', 'children': ['29', '43', '56', '63', '77', '87']}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '32', 'type': 'call', 'children': ['33', '36']}; {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'format_query'}; {'id': '36', 'type': 'argument_list', 'children': ['37', '38', '39', '40', '41']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'area'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'date'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'raw'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'area_relation'}; {'id': '41', 'type': 'dictionary_splat', 'children': ['42']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'keywords'}; {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'call', 'children': ['45', '50']}; {'id': '45', 'type': 'attribute', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '50', 'type': 'argument_list', 'children': ['51', '52', '53', '54', '55']}; {'id': '51', 'type': 'string', 'children': [], 'value': '"Running query: order_by=%s, limit=%s, offset=%s, query=%s"'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'order_by'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}; {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'formatted_order_by'}; {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': '_format_order_by'}; {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'order_by'}; {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '68']}; {'id': '65', 'type': 'pattern_list', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '68', 'type': 'call', 'children': ['69', '72']}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': '_load_query'}; {'id': '72', 'type': 'argument_list', 'children': ['73', '74', '75', '76']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'formatted_order_by'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'call', 'children': ['79', '84']}; {'id': '79', 'type': 'attribute', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '84', 'type': 'argument_list', 'children': ['85', '86']}; {'id': '85', 'type': 'string', 'children': [], 'value': '"Found %s products"'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '87', 'type': 'return_statement', 'children': ['88']}; {'id': '88', 'type': 'call', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': '_parse_opensearch_response'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'response'} | def query(self, area=None, date=None, raw=None, area_relation='Intersects',
order_by=None, limit=None, offset=0, **keywords):
query = self.format_query(area, date, raw, area_relation, **keywords)
self.logger.debug("Running query: order_by=%s, limit=%s, offset=%s, query=%s",
order_by, limit, offset, query)
formatted_order_by = _format_order_by(order_by)
response, count = self._load_query(query, formatted_order_by, limit, offset)
self.logger.info("Found %s products", count)
return _parse_opensearch_response(response) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_suggested_type_names'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'schema'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'output_type'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '7', 'type': 'block', 'children': ['8', '128']}; {'id': '8', 'type': 'if_statement', 'children': ['9', '16']}; {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '11', 'type': 'argument_list', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'output_type'}; {'id': '13', 'type': 'tuple', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'GraphQLInterfaceType'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'GraphQLUnionType'}; {'id': '16', 'type': 'block', 'children': ['17', '21', '27', '94', '119', '126']}; {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'suggested_object_types'}; {'id': '20', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'interface_usage_count'}; {'id': '24', 'type': 'call', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'OrderedDict'}; {'id': '26', 'type': 'argument_list', 'children': []}; {'id': '27', 'type': 'for_statement', 'children': ['28', '29', '35']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'possible_type'}; {'id': '29', 'type': 'call', 'children': ['30', '33']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'schema'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'get_possible_types'}; {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'output_type'}; {'id': '35', 'type': 'block', 'children': ['36', '48', '57']}; {'id': '36', 'type': 'if_statement', 'children': ['37', '46']}; {'id': '37', 'type': 'not_operator', 'children': ['38']}; {'id': '38', 'type': 'call', 'children': ['39', '44']}; {'id': '39', 'type': 'attribute', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'possible_type'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '46', 'type': 'block', 'children': ['47']}; {'id': '47', 'type': 'return_statement', 'children': []}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}; {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'suggested_object_types'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'possible_type'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '57', 'type': 'for_statement', 'children': ['58', '59', '62']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'possible_interface'}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'possible_type'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'interfaces'}; {'id': '62', 'type': 'block', 'children': ['63', '75']}; {'id': '63', 'type': 'if_statement', 'children': ['64', '73']}; {'id': '64', 'type': 'not_operator', 'children': ['65']}; {'id': '65', 'type': 'call', 'children': ['66', '71']}; {'id': '66', 'type': 'attribute', 'children': ['67', '70']}; {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'possible_interface'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '73', 'type': 'block', 'children': ['74']}; {'id': '74', 'type': 'continue_statement', 'children': []}; {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '82']}; {'id': '77', 'type': 'subscript', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'interface_usage_count'}; {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'possible_interface'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '82', 'type': '()', 'children': ['83']}; {'id': '83', 'type': 'binary_operator', 'children': ['84', '93'], 'value': '+'}; {'id': '84', 'type': 'call', 'children': ['85', '88']}; {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'interface_usage_count'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '88', 'type': 'argument_list', 'children': ['89', '92']}; {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'possible_interface'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '92', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '93', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'suggested_interface_types'}; {'id': '97', 'type': 'call', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '99', 'type': 'argument_list', 'children': ['100', '108', '116']}; {'id': '100', 'type': 'call', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'interface_usage_count'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '107', 'type': 'argument_list', 'children': []}; {'id': '108', 'type': 'keyword_argument', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '110', 'type': 'lambda', 'children': ['111', '113']}; {'id': '111', 'type': 'lambda_parameters', 'children': ['112']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '113', 'type': 'subscript', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'interface_usage_count'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '116', 'type': 'keyword_argument', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '118', 'type': 'True', 'children': []}; {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'call', 'children': ['121', '124']}; {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'suggested_interface_types'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'extend'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'suggested_object_types'}; {'id': '126', 'type': 'return_statement', 'children': ['127']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'suggested_interface_types'}; {'id': '128', 'type': 'return_statement', 'children': ['129']}; {'id': '129', 'type': 'list', 'children': [], 'value': '[]'} | def get_suggested_type_names(schema, output_type, field_name):
if isinstance(output_type, (GraphQLInterfaceType, GraphQLUnionType)):
suggested_object_types = []
interface_usage_count = OrderedDict()
for possible_type in schema.get_possible_types(output_type):
if not possible_type.fields.get(field_name):
return
suggested_object_types.append(possible_type.name)
for possible_interface in possible_type.interfaces:
if not possible_interface.fields.get(field_name):
continue
interface_usage_count[possible_interface.name] = (
interface_usage_count.get(possible_interface.name, 0) + 1
)
suggested_interface_types = sorted(
list(interface_usage_count.keys()),
key=lambda k: interface_usage_count[k],
reverse=True,
)
suggested_interface_types.extend(suggested_object_types)
return suggested_interface_types
return [] |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'suggestion_list'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'inp'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '6', 'type': 'block', 'children': ['7', '13', '22', '59']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'options_by_distance'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'OrderedDict'}; {'id': '12', 'type': 'argument_list', 'children': []}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'input_threshold'}; {'id': '16', 'type': 'binary_operator', 'children': ['17', '21'], 'value': '/'}; {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'inp'}; {'id': '21', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '22', 'type': 'for_statement', 'children': ['23', '24', '25']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'option'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '25', 'type': 'block', 'children': ['26', '34', '48']}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'distance'}; {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'lexical_distance'}; {'id': '31', 'type': 'argument_list', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'inp'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'option'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}; {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'threshold'}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '39', 'type': 'argument_list', 'children': ['40', '41', '47']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'input_threshold'}; {'id': '41', 'type': 'binary_operator', 'children': ['42', '46'], 'value': '/'}; {'id': '42', 'type': 'call', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'option'}; {'id': '46', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '47', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '48', 'type': 'if_statement', 'children': ['49', '52']}; {'id': '49', 'type': 'comparison_operator', 'children': ['50', '51'], 'value': '<='}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'distance'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'threshold'}; {'id': '52', 'type': 'block', 'children': ['53']}; {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '58']}; {'id': '55', 'type': 'subscript', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'options_by_distance'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'option'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'distance'}; {'id': '59', 'type': 'return_statement', 'children': ['60']}; {'id': '60', 'type': 'call', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '71']}; {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'call', 'children': ['67', '70']}; {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'options_by_distance'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '70', 'type': 'argument_list', 'children': []}; {'id': '71', 'type': 'keyword_argument', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '73', 'type': 'lambda', 'children': ['74', '76']}; {'id': '74', 'type': 'lambda_parameters', 'children': ['75']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '76', 'type': 'subscript', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'options_by_distance'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'k'} | def suggestion_list(inp, options):
options_by_distance = OrderedDict()
input_threshold = len(inp) / 2
for option in options:
distance = lexical_distance(inp, option)
threshold = max(input_threshold, len(option) / 2, 1)
if distance <= threshold:
options_by_distance[option] = distance
return sorted(
list(options_by_distance.keys()), key=lambda k: options_by_distance[k]
) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'lexical_distance'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '6', 'type': 'block', 'children': ['7', '26', '35', '80', '221']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '10', 'type': 'boolean_operator', 'children': ['11', '25'], 'value': 'or'}; {'id': '11', 'type': 'list_comprehension', 'children': ['12', '14']}; {'id': '12', 'type': 'list', 'children': ['13'], 'value': '[i]'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '14', 'type': 'for_in_clause', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '16', 'type': 'call', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '18', 'type': 'argument_list', 'children': ['19']}; {'id': '19', 'type': 'binary_operator', 'children': ['20', '24'], 'value': '+'}; {'id': '20', 'type': 'call', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '24', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '25', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'd_len'}; {'id': '29', 'type': 'boolean_operator', 'children': ['30', '34'], 'value': 'or'}; {'id': '30', 'type': 'call', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '32', 'type': 'argument_list', 'children': ['33']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '34', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '35', 'type': 'for_statement', 'children': ['36', '37', '41']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'd_len'}; {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'for_statement', 'children': ['43', '44', '54']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '46', 'type': 'argument_list', 'children': ['47', '48']}; {'id': '47', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '48', 'type': 'binary_operator', 'children': ['49', '53'], 'value': '+'}; {'id': '49', 'type': 'call', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '53', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '54', 'type': 'block', 'children': ['55']}; {'id': '55', 'type': 'if_statement', 'children': ['56', '59', '69']}; {'id': '56', 'type': 'comparison_operator', 'children': ['57', '58'], 'value': '=='}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '58', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '59', 'type': 'block', 'children': ['60']}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}; {'id': '61', 'type': 'call', 'children': ['62', '67']}; {'id': '62', 'type': 'attribute', 'children': ['63', '66']}; {'id': '63', 'type': 'subscript', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '69', 'type': 'else_clause', 'children': ['70']}; {'id': '70', 'type': 'block', 'children': ['71']}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'call', 'children': ['73', '78']}; {'id': '73', 'type': 'attribute', 'children': ['74', '77']}; {'id': '74', 'type': 'subscript', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}; {'id': '79', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '80', 'type': 'for_statement', 'children': ['81', '82', '92']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '82', 'type': 'call', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '84', 'type': 'argument_list', 'children': ['85', '86']}; {'id': '85', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '86', 'type': 'binary_operator', 'children': ['87', '91'], 'value': '+'}; {'id': '87', 'type': 'call', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '91', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '92', 'type': 'block', 'children': ['93']}; {'id': '93', 'type': 'for_statement', 'children': ['94', '95', '105']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '95', 'type': 'call', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '97', 'type': 'argument_list', 'children': ['98', '99']}; {'id': '98', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '99', 'type': 'binary_operator', 'children': ['100', '104'], 'value': '+'}; {'id': '100', 'type': 'call', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '104', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '105', 'type': 'block', 'children': ['106', '123', '162']}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}; {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'cost'}; {'id': '109', 'type': 'conditional_expression', 'children': ['110', '111', '122'], 'value': 'if'}; {'id': '110', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '111', 'type': 'comparison_operator', 'children': ['112', '117'], 'value': '=='}; {'id': '112', 'type': 'subscript', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '114', 'type': 'binary_operator', 'children': ['115', '116'], 'value': '-'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '116', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '117', 'type': 'subscript', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '119', 'type': 'binary_operator', 'children': ['120', '121'], 'value': '-'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '121', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '130']}; {'id': '125', 'type': 'subscript', 'children': ['126', '129']}; {'id': '126', 'type': 'subscript', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '130', 'type': 'call', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'min'}; {'id': '132', 'type': 'argument_list', 'children': ['133', '142', '151']}; {'id': '133', 'type': 'binary_operator', 'children': ['134', '141'], 'value': '+'}; {'id': '134', 'type': 'subscript', 'children': ['135', '140']}; {'id': '135', 'type': 'subscript', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '137', 'type': 'binary_operator', 'children': ['138', '139'], 'value': '-'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '139', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '141', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '142', 'type': 'binary_operator', 'children': ['143', '150'], 'value': '+'}; {'id': '143', 'type': 'subscript', 'children': ['144', '147']}; {'id': '144', 'type': 'subscript', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '147', 'type': 'binary_operator', 'children': ['148', '149'], 'value': '-'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '149', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '150', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '151', 'type': 'binary_operator', 'children': ['152', '161'], 'value': '+'}; {'id': '152', 'type': 'subscript', 'children': ['153', '158']}; {'id': '153', 'type': 'subscript', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '155', 'type': 'binary_operator', 'children': ['156', '157'], 'value': '-'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '157', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '158', 'type': 'binary_operator', 'children': ['159', '160'], 'value': '-'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '160', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'cost'}; {'id': '162', 'type': 'if_statement', 'children': ['163', '194']}; {'id': '163', 'type': 'boolean_operator', 'children': ['164', '183'], 'value': 'and'}; {'id': '164', 'type': 'boolean_operator', 'children': ['165', '172'], 'value': 'and'}; {'id': '165', 'type': 'boolean_operator', 'children': ['166', '169'], 'value': 'and'}; {'id': '166', 'type': 'comparison_operator', 'children': ['167', '168'], 'value': '>'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '168', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '169', 'type': 'comparison_operator', 'children': ['170', '171'], 'value': '<'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '171', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '172', 'type': 'comparison_operator', 'children': ['173', '178'], 'value': '=='}; {'id': '173', 'type': 'subscript', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '175', 'type': 'binary_operator', 'children': ['176', '177'], 'value': '-'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '177', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '178', 'type': 'subscript', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '180', 'type': 'binary_operator', 'children': ['181', '182'], 'value': '-'}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '182', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '183', 'type': 'comparison_operator', 'children': ['184', '189'], 'value': '=='}; {'id': '184', 'type': 'subscript', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '186', 'type': 'binary_operator', 'children': ['187', '188'], 'value': '-'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '188', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '189', 'type': 'subscript', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '191', 'type': 'binary_operator', 'children': ['192', '193'], 'value': '-'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '193', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '194', 'type': 'block', 'children': ['195']}; {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '202']}; {'id': '197', 'type': 'subscript', 'children': ['198', '201']}; {'id': '198', 'type': 'subscript', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '202', 'type': 'call', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'min'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '210']}; {'id': '205', 'type': 'subscript', 'children': ['206', '209']}; {'id': '206', 'type': 'subscript', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '210', 'type': 'binary_operator', 'children': ['211', '220'], 'value': '+'}; {'id': '211', 'type': 'subscript', 'children': ['212', '217']}; {'id': '212', 'type': 'subscript', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '214', 'type': 'binary_operator', 'children': ['215', '216'], 'value': '-'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '216', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '217', 'type': 'binary_operator', 'children': ['218', '219'], 'value': '-'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '219', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'cost'}; {'id': '221', 'type': 'return_statement', 'children': ['222']}; {'id': '222', 'type': 'subscript', 'children': ['223', '229']}; {'id': '223', 'type': 'subscript', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '225', 'type': 'call', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '227', 'type': 'argument_list', 'children': ['228']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '229', 'type': 'call', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '231', 'type': 'argument_list', 'children': ['232']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'b'} | def lexical_distance(a, b):
d = [[i] for i in range(len(a) + 1)] or []
d_len = len(d) or 1
for i in range(d_len):
for j in range(1, len(b) + 1):
if i == 0:
d[i].append(j)
else:
d[i].append(0)
for i in range(1, len(a) + 1):
for j in range(1, len(b) + 1):
cost = 0 if a[i - 1] == b[j - 1] else 1
d[i][j] = min(d[i - 1][j] + 1, d[i][j - 1] + 1, d[i - 1][j - 1] + cost)
if i > 1 and j < 1 and a[i - 1] == b[j - 2] and a[i - 2] == b[j - 1]:
d[i][j] = min(d[i][j], d[i - 2][j - 2] + cost)
return d[len(a)][len(b)] |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'arrange'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '5', 'type': 'list_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '7', 'type': 'dictionary_splat_pattern', 'children': ['8']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '9', 'type': 'block', 'children': ['10', '21', '56', '75', '92']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}; {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'flat_args'}; {'id': '13', 'type': 'list_comprehension', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '15', 'type': 'for_in_clause', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'flatten'}; {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'series'}; {'id': '24', 'type': 'list_comprehension', 'children': ['25', '53']}; {'id': '25', 'type': 'conditional_expression', 'children': ['26', '29', '34'], 'value': 'if'}; {'id': '26', 'type': 'subscript', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '31', 'type': 'argument_list', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '34', 'type': 'conditional_expression', 'children': ['35', '42', '47'], 'value': 'if'}; {'id': '35', 'type': 'subscript', 'children': ['36', '39', '41']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'iloc'}; {'id': '39', 'type': 'slice', 'children': ['40']}; {'id': '40', 'type': 'colon', 'children': []}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '42', 'type': 'call', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '44', 'type': 'argument_list', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'Series'}; {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '53', 'type': 'for_in_clause', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'flat_args'}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}; {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '59', 'type': 'call', 'children': ['60', '71']}; {'id': '60', 'type': 'attribute', 'children': ['61', '70']}; {'id': '61', 'type': 'call', 'children': ['62', '65']}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'concat'}; {'id': '65', 'type': 'argument_list', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'series'}; {'id': '67', 'type': 'keyword_argument', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '69', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'reset_index'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'keyword_argument', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'drop'}; {'id': '74', 'type': 'True', 'children': []}; {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '78', 'type': 'call', 'children': ['79', '82']}; {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'sort_values'}; {'id': '82', 'type': 'argument_list', 'children': ['83', '90']}; {'id': '83', 'type': 'call', 'children': ['84', '89']}; {'id': '84', 'type': 'attribute', 'children': ['85', '88']}; {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'tolist'}; {'id': '89', 'type': 'argument_list', 'children': []}; {'id': '90', 'type': 'dictionary_splat', 'children': ['91']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '92', 'type': 'return_statement', 'children': ['93']}; {'id': '93', 'type': 'subscript', 'children': ['94', '97', '100']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'iloc'}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '100', 'type': 'slice', 'children': ['101']}; {'id': '101', 'type': 'colon', 'children': []} | def arrange(df, *args, **kwargs):
flat_args = [a for a in flatten(args)]
series = [df[arg] if isinstance(arg, str) else
df.iloc[:, arg] if isinstance(arg, int) else
pd.Series(arg) for arg in flat_args]
sorter = pd.concat(series, axis=1).reset_index(drop=True)
sorter = sorter.sort_values(sorter.columns.tolist(), **kwargs)
return df.iloc[sorter.index, :] |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'csort'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'objs'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '6', 'type': 'block', 'children': ['7', '24']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'idxs'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '12', 'type': 'generator_expression', 'children': ['13', '16']}; {'id': '13', 'type': 'tuple', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '16', 'type': 'for_in_clause', 'children': ['17', '20']}; {'id': '17', 'type': 'tuple_pattern', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '20', 'type': 'call', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'objs'}; {'id': '24', 'type': 'return_statement', 'children': ['25']}; {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '27', 'type': 'argument_list', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'objs'}; {'id': '29', 'type': 'keyword_argument', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '31', 'type': 'lambda', 'children': ['32', '34']}; {'id': '32', 'type': 'lambda_parameters', 'children': ['33']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '34', 'type': 'tuple', 'children': ['35', '39']}; {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '39', 'type': 'subscript', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'idxs'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'obj'} | def csort(objs, key):
idxs = dict((obj, i) for (i, obj) in enumerate(objs))
return sorted(objs, key=lambda obj: (key(obj), idxs[obj])) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'fast_combine_pairs'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'files'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'force_single'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'full_name'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'separators'}; {'id': '8', 'type': 'block', 'children': ['9', '16', '26', '40', '51', '58', '85', '103']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'files'}; {'id': '12', 'type': 'call', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'sort_filenames'}; {'id': '14', 'type': 'argument_list', 'children': ['15']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'files'}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '19', 'type': 'call', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'tz'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'sliding_window'}; {'id': '23', 'type': 'argument_list', 'children': ['24', '25']}; {'id': '24', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'files'}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'pairs'}; {'id': '29', 'type': 'list_comprehension', 'children': ['30', '37']}; {'id': '30', 'type': 'call', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'combine_pairs'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '34', '35', '36']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'chunk'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'force_single'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'full_name'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'separators'}; {'id': '37', 'type': 'for_in_clause', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'chunk'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'chunks'}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'pairs'}; {'id': '43', 'type': 'list_comprehension', 'children': ['44', '45', '48']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '45', 'type': 'for_in_clause', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'pairs'}; {'id': '48', 'type': 'for_in_clause', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'longest'}; {'id': '54', 'type': 'call', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '58', 'type': 'for_statement', 'children': ['59', '60', '61']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'pair'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'pairs'}; {'id': '61', 'type': 'block', 'children': ['62']}; {'id': '62', 'type': 'for_statement', 'children': ['63', '64', '65']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'file'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'pair'}; {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'if_statement', 'children': ['67', '78']}; {'id': '67', 'type': 'comparison_operator', 'children': ['68', '74'], 'value': '<'}; {'id': '68', 'type': 'call', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}; {'id': '71', 'type': 'subscript', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'longest'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'file'}; {'id': '74', 'type': 'call', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'pair'}; {'id': '78', 'type': 'block', 'children': ['79']}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '84']}; {'id': '81', 'type': 'subscript', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'longest'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'file'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'pair'}; {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'longest'}; {'id': '88', 'type': 'set_comprehension', 'children': ['89', '96']}; {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'call', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'sort_filenames'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '96', 'type': 'for_in_clause', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '98', 'type': 'call', 'children': ['99', '102']}; {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'longest'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '102', 'type': 'argument_list', 'children': []}; {'id': '103', 'type': 'return_statement', 'children': ['104']}; {'id': '104', 'type': 'list_comprehension', 'children': ['105', '112']}; {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'sort_filenames'}; {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'call', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '112', 'type': 'for_in_clause', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'longest'} | def fast_combine_pairs(files, force_single, full_name, separators):
files = sort_filenames(files)
chunks = tz.sliding_window(10, files)
pairs = [combine_pairs(chunk, force_single, full_name, separators) for chunk in chunks]
pairs = [y for x in pairs for y in x]
longest = defaultdict(list)
for pair in pairs:
for file in pair:
if len(longest[file]) < len(pair):
longest[file] = pair
longest = {tuple(sort_filenames(x)) for x in longest.values()}
return [sort_filenames(list(x)) for x in longest] |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'align_bam'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'align_dir'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '9', 'type': 'block', 'children': ['10', '16', '35', '45', '55', '65', '77', '98', '219']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}; {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '13', 'type': 'subscript', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '15', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '19', 'type': 'call', 'children': ['20', '25']}; {'id': '20', 'type': 'attribute', 'children': ['21', '24']}; {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '25', 'type': 'argument_list', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'align_dir'}; {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'string', 'children': [], 'value': '"{0}-sort.bam"'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'subscript', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '34', 'type': 'string', 'children': [], 'value': '"lane"'}; {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'samtools'}; {'id': '38', 'type': 'call', 'children': ['39', '42']}; {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'get_program'}; {'id': '42', 'type': 'argument_list', 'children': ['43', '44']}; {'id': '43', 'type': 'string', 'children': [], 'value': '"samtools"'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'bedtools'}; {'id': '48', 'type': 'call', 'children': ['49', '52']}; {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'get_program'}; {'id': '52', 'type': 'argument_list', 'children': ['53', '54']}; {'id': '53', 'type': 'string', 'children': [], 'value': '"bedtools"'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'resources'}; {'id': '58', 'type': 'call', 'children': ['59', '62']}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'get_resources'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '64']}; {'id': '63', 'type': 'string', 'children': [], 'value': '"samtools"'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'num_cores'}; {'id': '68', 'type': 'call', 'children': ['69', '74']}; {'id': '69', 'type': 'attribute', 'children': ['70', '73']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '72', 'type': 'string', 'children': [], 'value': '"algorithm"'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '74', 'type': 'argument_list', 'children': ['75', '76']}; {'id': '75', 'type': 'string', 'children': [], 'value': '"num_cores"'}; {'id': '76', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'max_mem'}; {'id': '80', 'type': 'call', 'children': ['81', '97']}; {'id': '81', 'type': 'attribute', 'children': ['82', '96']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'adjust_memory'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '94', '95']}; {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'resources'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '91', 'type': 'argument_list', 'children': ['92', '93']}; {'id': '92', 'type': 'string', 'children': [], 'value': '"memory"'}; {'id': '93', 'type': 'string', 'children': [], 'value': '"1G"'}; {'id': '94', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '95', 'type': 'string', 'children': [], 'value': '"decrease"'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '97', 'type': 'argument_list', 'children': []}; {'id': '98', 'type': 'if_statement', 'children': ['99', '106']}; {'id': '99', 'type': 'not_operator', 'children': ['100']}; {'id': '100', 'type': 'call', 'children': ['101', '104']}; {'id': '101', 'type': 'attribute', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '104', 'type': 'argument_list', 'children': ['105']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '106', 'type': 'block', 'children': ['107']}; {'id': '107', 'type': 'with_statement', 'children': ['108', '117']}; {'id': '108', 'type': 'with_clause', 'children': ['109']}; {'id': '109', 'type': 'with_item', 'children': ['110']}; {'id': '110', 'type': 'as_pattern', 'children': ['111', '115']}; {'id': '111', 'type': 'call', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'tx_tmpdir'}; {'id': '113', 'type': 'argument_list', 'children': ['114']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '115', 'type': 'as_pattern_target', 'children': ['116']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'work_dir'}; {'id': '117', 'type': 'block', 'children': ['118']}; {'id': '118', 'type': 'with_statement', 'children': ['119', '139']}; {'id': '119', 'type': 'with_clause', 'children': ['120']}; {'id': '120', 'type': 'with_item', 'children': ['121']}; {'id': '121', 'type': 'as_pattern', 'children': ['122', '135']}; {'id': '122', 'type': 'call', 'children': ['123', '126']}; {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'postalign'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'tobam_cl'}; {'id': '126', 'type': 'argument_list', 'children': ['127', '128', '129']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '129', 'type': 'call', 'children': ['130', '133']}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'bam'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'is_paired'}; {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '135', 'type': 'as_pattern_target', 'children': ['136']}; {'id': '136', 'type': 'tuple', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'tobam_cl'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '139', 'type': 'block', 'children': ['140', '150', '163', '169', '178', '192']}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}; {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'bwa_cmd'}; {'id': '143', 'type': 'call', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': '_get_bwa_mem_cmd'}; {'id': '145', 'type': 'argument_list', 'children': ['146', '147', '148', '149']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '149', 'type': 'string', 'children': [], 'value': '"-"'}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}; {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'tx_out_prefix'}; {'id': '153', 'type': 'subscript', 'children': ['154', '162']}; {'id': '154', 'type': 'call', 'children': ['155', '160']}; {'id': '155', 'type': 'attribute', 'children': ['156', '159']}; {'id': '156', 'type': 'attribute', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'splitext'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '162', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'prefix1'}; {'id': '166', 'type': 'binary_operator', 'children': ['167', '168'], 'value': '%'}; {'id': '167', 'type': 'string', 'children': [], 'value': '"%s-in1"'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'tx_out_prefix'}; {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '172', 'type': '()', 'children': ['173']}; {'id': '173', 'type': 'concatenated_string', 'children': ['174', '175', '176', '177']}; {'id': '174', 'type': 'string', 'children': [], 'value': '"unset JAVA_HOME && "'}; {'id': '175', 'type': 'string', 'children': [], 'value': '"{samtools} sort -n -o -l 1 -@ {num_cores} -m {max_mem} {in_bam} {prefix1} "'}; {'id': '176', 'type': 'string', 'children': [], 'value': '"| {bedtools} bamtofastq -i /dev/stdin -fq /dev/stdout -fq2 /dev/stdout "'}; {'id': '177', 'type': 'string', 'children': [], 'value': '"| {bwa_cmd} | "'}; {'id': '178', 'type': 'expression_statement', 'children': ['179']}; {'id': '179', 'type': 'assignment', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '181', 'type': 'binary_operator', 'children': ['182', '191'], 'value': '+'}; {'id': '182', 'type': 'call', 'children': ['183', '186']}; {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '186', 'type': 'argument_list', 'children': ['187']}; {'id': '187', 'type': 'dictionary_splat', 'children': ['188']}; {'id': '188', 'type': 'call', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '190', 'type': 'argument_list', 'children': []}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'tobam_cl'}; {'id': '192', 'type': 'expression_statement', 'children': ['193']}; {'id': '193', 'type': 'call', 'children': ['194', '197']}; {'id': '194', 'type': 'attribute', 'children': ['195', '196']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'do'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '197', 'type': 'argument_list', 'children': ['198', '199', '204', '205']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '199', 'type': 'binary_operator', 'children': ['200', '201'], 'value': '%'}; {'id': '200', 'type': 'string', 'children': [], 'value': '"bwa mem alignment from BAM: %s"'}; {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '203', 'type': 'string', 'children': [], 'value': '"sample"'}; {'id': '204', 'type': 'None', 'children': []}; {'id': '205', 'type': 'list', 'children': ['206', '212'], 'value': '[do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, in_bam)]'}; {'id': '206', 'type': 'call', 'children': ['207', '210']}; {'id': '207', 'type': 'attribute', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'do'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'file_nonempty'}; {'id': '210', 'type': 'argument_list', 'children': ['211']}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '212', 'type': 'call', 'children': ['213', '216']}; {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'do'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'file_reasonable_size'}; {'id': '216', 'type': 'argument_list', 'children': ['217', '218']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '219', 'type': 'return_statement', 'children': ['220']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'out_file'} | def align_bam(in_bam, ref_file, names, align_dir, data):
config = data["config"]
out_file = os.path.join(align_dir, "{0}-sort.bam".format(names["lane"]))
samtools = config_utils.get_program("samtools", config)
bedtools = config_utils.get_program("bedtools", config)
resources = config_utils.get_resources("samtools", config)
num_cores = config["algorithm"].get("num_cores", 1)
max_mem = config_utils.adjust_memory(resources.get("memory", "1G"),
3, "decrease").upper()
if not utils.file_exists(out_file):
with tx_tmpdir(data) as work_dir:
with postalign.tobam_cl(data, out_file, bam.is_paired(in_bam)) as (tobam_cl, tx_out_file):
bwa_cmd = _get_bwa_mem_cmd(data, out_file, ref_file, "-")
tx_out_prefix = os.path.splitext(tx_out_file)[0]
prefix1 = "%s-in1" % tx_out_prefix
cmd = ("unset JAVA_HOME && "
"{samtools} sort -n -o -l 1 -@ {num_cores} -m {max_mem} {in_bam} {prefix1} "
"| {bedtools} bamtofastq -i /dev/stdin -fq /dev/stdout -fq2 /dev/stdout "
"| {bwa_cmd} | ")
cmd = cmd.format(**locals()) + tobam_cl
do.run(cmd, "bwa mem alignment from BAM: %s" % names["sample"], None,
[do.file_nonempty(tx_out_file), do.file_reasonable_size(tx_out_file, in_bam)])
return out_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_combine_regions'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'all_regions'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'ref_regions'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '28', '47', '51', '81', '90', '106']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'chrom_order'}; {'id': '10', 'type': 'dictionary', 'children': []}; {'id': '11', 'type': 'for_statement', 'children': ['12', '15', '19']}; {'id': '12', 'type': 'pattern_list', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '15', 'type': 'call', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '17', 'type': 'argument_list', 'children': ['18']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'ref_regions'}; {'id': '19', 'type': 'block', 'children': ['20']}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}; {'id': '21', 'type': 'assignment', 'children': ['22', '27']}; {'id': '22', 'type': 'subscript', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'chrom_order'}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '28', 'type': 'function_definition', 'children': ['29', '30', '32']}; {'id': '29', 'type': 'function_name', 'children': [], 'value': 'wchrom_key'}; {'id': '30', 'type': 'parameters', 'children': ['31']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '32', 'type': 'block', 'children': ['33', '40']}; {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '39']}; {'id': '35', 'type': 'pattern_list', 'children': ['36', '37', '38']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '40', 'type': 'return_statement', 'children': ['41']}; {'id': '41', 'type': 'tuple', 'children': ['42', '45', '46']}; {'id': '42', 'type': 'subscript', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'chrom_order'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'all_intervals'}; {'id': '50', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '51', 'type': 'for_statement', 'children': ['52', '53', '54']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'region_group'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'all_regions'}; {'id': '54', 'type': 'block', 'children': ['55']}; {'id': '55', 'type': 'for_statement', 'children': ['56', '57', '58']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'region_group'}; {'id': '58', 'type': 'block', 'children': ['59']}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'call', 'children': ['61', '64']}; {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'all_intervals'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'tuple', 'children': ['66', '69', '75']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'all_intervals'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'keyword_argument', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'wchrom_key'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}; {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'bed_lines'}; {'id': '93', 'type': 'list_comprehension', 'children': ['94', '100']}; {'id': '94', 'type': 'binary_operator', 'children': ['95', '96'], 'value': '%'}; {'id': '95', 'type': 'string', 'children': [], 'value': '"%s\\t%s\\t%s"'}; {'id': '96', 'type': 'tuple', 'children': ['97', '98', '99']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '100', 'type': 'for_in_clause', 'children': ['101', '105']}; {'id': '101', 'type': 'tuple_pattern', 'children': ['102', '103', '104']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'all_intervals'}; {'id': '106', 'type': 'return_statement', 'children': ['107']}; {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'pybedtools'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'BedTool'}; {'id': '111', 'type': 'argument_list', 'children': ['112', '118']}; {'id': '112', 'type': 'call', 'children': ['113', '116']}; {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'string', 'children': [], 'value': '"\\n"'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '116', 'type': 'argument_list', 'children': ['117']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'bed_lines'}; {'id': '118', 'type': 'keyword_argument', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'from_string'}; {'id': '120', 'type': 'True', 'children': []} | def _combine_regions(all_regions, ref_regions):
chrom_order = {}
for i, x in enumerate(ref_regions):
chrom_order[x.chrom] = i
def wchrom_key(x):
chrom, start, end = x
return (chrom_order[chrom], start, end)
all_intervals = []
for region_group in all_regions:
for region in region_group:
all_intervals.append((region.chrom, int(region.start), int(region.stop)))
all_intervals.sort(key=wchrom_key)
bed_lines = ["%s\t%s\t%s" % (c, s, e) for (c, s, e) in all_intervals]
return pybedtools.BedTool("\n".join(bed_lines), from_string=True) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_add_meta'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'xs'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'block', 'children': ['12', '16', '153']}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}; {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '15', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '16', 'type': 'for_statement', 'children': ['17', '18', '19']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'xs'}; {'id': '19', 'type': 'block', 'children': ['20', '51', '64', '100', '146']}; {'id': '20', 'type': 'if_statement', 'children': ['21', '43']}; {'id': '21', 'type': 'boolean_operator', 'children': ['22', '32'], 'value': 'or'}; {'id': '22', 'type': 'not_operator', 'children': ['23']}; {'id': '23', 'type': 'call', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '25', 'type': 'argument_list', 'children': ['26', '29']}; {'id': '26', 'type': 'subscript', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '28', 'type': 'string', 'children': [], 'value': '"path"'}; {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'six'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'string_types'}; {'id': '32', 'type': 'not_operator', 'children': ['33']}; {'id': '33', 'type': 'call', 'children': ['34', '39']}; {'id': '34', 'type': 'attribute', 'children': ['35', '38']}; {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'subscript', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '42', 'type': 'string', 'children': [], 'value': '"path"'}; {'id': '43', 'type': 'block', 'children': ['44']}; {'id': '44', 'type': 'raise_statement', 'children': ['45']}; {'id': '45', 'type': 'call', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'binary_operator', 'children': ['49', '50'], 'value': '%'}; {'id': '49', 'type': 'string', 'children': [], 'value': '"Unexpected path for upload: %s"'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '56']}; {'id': '53', 'type': 'subscript', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '55', 'type': 'string', 'children': [], 'value': '"mtime"'}; {'id': '56', 'type': 'call', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'shared'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'get_file_timestamp'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'subscript', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '63', 'type': 'string', 'children': [], 'value': '"path"'}; {'id': '64', 'type': 'if_statement', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '66', 'type': 'block', 'children': ['67', '76']}; {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'sample_name'}; {'id': '70', 'type': 'call', 'children': ['71', '74']}; {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'get_sample_name'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '76', 'type': 'if_statement', 'children': ['77', '80', '87']}; {'id': '77', 'type': 'comparison_operator', 'children': ['78', '79'], 'value': 'not'}; {'id': '78', 'type': 'string', 'children': [], 'value': '"sample"'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '80', 'type': 'block', 'children': ['81']}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '86']}; {'id': '83', 'type': 'subscript', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '85', 'type': 'string', 'children': [], 'value': '"sample"'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'sample_name'}; {'id': '87', 'type': 'elif_clause', 'children': ['88', '93']}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '92'], 'value': '!='}; {'id': '89', 'type': 'subscript', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '91', 'type': 'string', 'children': [], 'value': '"sample"'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'sample_name'}; {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'assignment', 'children': ['96', '99']}; {'id': '96', 'type': 'subscript', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '98', 'type': 'string', 'children': [], 'value': '"run"'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'sample_name'}; {'id': '100', 'type': 'if_statement', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '102', 'type': 'block', 'children': ['103', '114', '136']}; {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'fc_name'}; {'id': '106', 'type': 'boolean_operator', 'children': ['107', '113'], 'value': 'or'}; {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'string', 'children': [], 'value': '"fc_name"'}; {'id': '113', 'type': 'string', 'children': [], 'value': '"project"'}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}; {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'fc_date'}; {'id': '117', 'type': 'boolean_operator', 'children': ['118', '124'], 'value': 'or'}; {'id': '118', 'type': 'call', 'children': ['119', '122']}; {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}; {'id': '123', 'type': 'string', 'children': [], 'value': '"fc_date"'}; {'id': '124', 'type': 'call', 'children': ['125', '134']}; {'id': '125', 'type': 'attribute', 'children': ['126', '133']}; {'id': '126', 'type': 'call', 'children': ['127', '132']}; {'id': '127', 'type': 'attribute', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'datetime'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'datetime'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'now'}; {'id': '132', 'type': 'argument_list', 'children': []}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'strftime'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}; {'id': '135', 'type': 'string', 'children': [], 'value': '"%Y-%m-%d"'}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}; {'id': '137', 'type': 'assignment', 'children': ['138', '141']}; {'id': '138', 'type': 'subscript', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '140', 'type': 'string', 'children': [], 'value': '"run"'}; {'id': '141', 'type': 'binary_operator', 'children': ['142', '143'], 'value': '%'}; {'id': '142', 'type': 'string', 'children': [], 'value': '"%s_%s"'}; {'id': '143', 'type': 'tuple', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'fc_date'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'fc_name'}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '151', 'type': 'argument_list', 'children': ['152']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '153', 'type': 'return_statement', 'children': ['154']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'out'} | def _add_meta(xs, sample=None, config=None):
out = []
for x in xs:
if not isinstance(x["path"], six.string_types) or not os.path.exists(x["path"]):
raise ValueError("Unexpected path for upload: %s" % x)
x["mtime"] = shared.get_file_timestamp(x["path"])
if sample:
sample_name = dd.get_sample_name(sample)
if "sample" not in x:
x["sample"] = sample_name
elif x["sample"] != sample_name:
x["run"] = sample_name
if config:
fc_name = config.get("fc_name") or "project"
fc_date = config.get("fc_date") or datetime.datetime.now().strftime("%Y-%m-%d")
x["run"] = "%s_%s" % (fc_date, fc_name)
out.append(x)
return out |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'report'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '10', '11']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'is_paired'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'bait_file'}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'target_file'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'variant_region_file'}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '12', 'type': 'block', 'children': ['13', '22', '32', '36', '46', '60', '144', '153', '168', '172', '193', '214']}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'dup_metrics'}; {'id': '16', 'type': 'call', 'children': ['17', '20']}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': '_get_current_dup_metrics'}; {'id': '20', 'type': 'argument_list', 'children': ['21']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'align_metrics'}; {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': '_collect_align_metrics'}; {'id': '29', 'type': 'argument_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'gc_graph'}; {'id': '35', 'type': 'None', 'children': []}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}; {'id': '37', 'type': 'assignment', 'children': ['38', '42']}; {'id': '38', 'type': 'pattern_list', 'children': ['39', '40', '41']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'insert_graph'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'insert_metrics'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'hybrid_metrics'}; {'id': '42', 'type': 'tuple', 'children': ['43', '44', '45']}; {'id': '43', 'type': 'None', 'children': []}; {'id': '44', 'type': 'None', 'children': []}; {'id': '45', 'type': 'None', 'children': []}; {'id': '46', 'type': 'if_statement', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'is_paired'}; {'id': '48', 'type': 'block', 'children': ['49']}; {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '54']}; {'id': '51', 'type': 'pattern_list', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'insert_graph'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'insert_metrics'}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': '_insert_sizes'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '60', 'type': 'if_statement', 'children': ['61', '64', '100']}; {'id': '61', 'type': 'boolean_operator', 'children': ['62', '63'], 'value': 'and'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'bait_file'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'target_file'}; {'id': '64', 'type': 'block', 'children': ['65', '77', '89']}; {'id': '65', 'type': 'assert_statement', 'children': ['66', '74']}; {'id': '66', 'type': 'call', 'children': ['67', '72']}; {'id': '67', 'type': 'attribute', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '72', 'type': 'argument_list', 'children': ['73']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'bait_file'}; {'id': '74', 'type': 'tuple', 'children': ['75', '76']}; 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{'id': '90', 'type': 'assignment', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'hybrid_metrics'}; {'id': '92', 'type': 'call', 'children': ['93', '96']}; {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': '_hybrid_select_metrics'}; {'id': '96', 'type': 'argument_list', 'children': ['97', '98', '99']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'bait_file'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'target_file'}; {'id': '100', 'type': 'elif_clause', 'children': ['101', '120']}; {'id': '101', 'type': '()', 'children': ['102']}; {'id': '102', 'type': 'boolean_operator', 'children': ['103', '104'], 'value': 'and'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'variant_region_file'}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '118'], 'value': 'in'}; {'id': '105', 'type': 'call', 'children': ['106', '117']}; {'id': '106', 'type': 'attribute', 'children': ['107', '116']}; {'id': '107', 'type': 'call', 'children': ['108', '113']}; {'id': '108', 'type': 'attribute', 'children': ['109', '112']}; {'id': '109', 'type': 'subscript', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '111', 'type': 'string', 'children': [], 'value': '"algorithm"'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '113', 'type': 'argument_list', 'children': ['114', '115']}; {'id': '114', 'type': 'string', 'children': [], 'value': '"coverage_interval"'}; {'id': '115', 'type': 'string', 'children': [], 'value': '""'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'lower'}; {'id': '117', 'type': 'argument_list', 'children': []}; {'id': '118', 'type': 'list', 'children': ['119'], 'value': '["exome"]'}; {'id': '119', 'type': 'string', 'children': [], 'value': '"exome"'}; 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{'id': '135', 'type': 'identifier', 'children': [], 'value': 'hybrid_metrics'}; {'id': '136', 'type': 'call', 'children': ['137', '140']}; {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': '_hybrid_select_metrics'}; {'id': '140', 'type': 'argument_list', 'children': ['141', '142', '143']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'variant_region_file'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'variant_region_file'}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}; {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'vrn_vals'}; {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': '_variant_eval_metrics'}; {'id': '151', 'type': 'argument_list', 'children': ['152']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'assignment', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'summary_info'}; {'id': '156', 'type': 'call', 'children': ['157', '162']}; {'id': '157', 'type': 'attribute', 'children': ['158', '161']}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': '_parser'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'get_summary_metrics'}; {'id': '162', 'type': 'argument_list', 'children': ['163', '164', '165', '166', '167']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'align_metrics'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'dup_metrics'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'insert_metrics'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'hybrid_metrics'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'vrn_vals'}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}; {'id': '169', 'type': 'assignment', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'graphs'}; {'id': '171', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '172', 'type': 'if_statement', 'children': ['173', '183']}; {'id': '173', 'type': 'boolean_operator', 'children': ['174', '175'], 'value': 'and'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'gc_graph'}; {'id': '175', 'type': 'call', 'children': ['176', '181']}; {'id': '176', 'type': 'attribute', 'children': ['177', '180']}; {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '181', 'type': 'argument_list', 'children': ['182']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'gc_graph'}; {'id': '183', 'type': 'block', 'children': ['184']}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}; {'id': '185', 'type': 'call', 'children': ['186', '189']}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'graphs'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '189', 'type': 'argument_list', 'children': ['190']}; {'id': '190', 'type': 'tuple', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'gc_graph'}; {'id': '192', 'type': 'string', 'children': [], 'value': '"Distribution of GC content across reads"'}; {'id': '193', 'type': 'if_statement', 'children': ['194', '204']}; {'id': '194', 'type': 'boolean_operator', 'children': ['195', '196'], 'value': 'and'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'insert_graph'}; {'id': '196', 'type': 'call', 'children': ['197', '202']}; {'id': '197', 'type': 'attribute', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '202', 'type': 'argument_list', 'children': ['203']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'insert_graph'}; {'id': '204', 'type': 'block', 'children': ['205']}; {'id': '205', 'type': 'expression_statement', 'children': ['206']}; {'id': '206', 'type': 'call', 'children': ['207', '210']}; {'id': '207', 'type': 'attribute', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'graphs'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '210', 'type': 'argument_list', 'children': ['211']}; {'id': '211', 'type': 'tuple', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'insert_graph'}; {'id': '213', 'type': 'string', 'children': [], 'value': '"Distribution of paired end insert sizes"'}; {'id': '214', 'type': 'return_statement', 'children': ['215']}; {'id': '215', 'type': 'expression_list', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'summary_info'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'graphs'} | def report(self, align_bam, ref_file, is_paired, bait_file, target_file,
variant_region_file, config):
dup_metrics = self._get_current_dup_metrics(align_bam)
align_metrics = self._collect_align_metrics(align_bam, ref_file)
gc_graph = None
insert_graph, insert_metrics, hybrid_metrics = (None, None, None)
if is_paired:
insert_graph, insert_metrics = self._insert_sizes(align_bam)
if bait_file and target_file:
assert os.path.exists(bait_file), (bait_file, "does not exist!")
assert os.path.exists(target_file), (target_file, "does not exist!")
hybrid_metrics = self._hybrid_select_metrics(align_bam,
bait_file, target_file)
elif (variant_region_file and
config["algorithm"].get("coverage_interval", "").lower() in ["exome"]):
assert os.path.exists(variant_region_file), (variant_region_file, "does not exist")
hybrid_metrics = self._hybrid_select_metrics(
align_bam, variant_region_file, variant_region_file)
vrn_vals = self._variant_eval_metrics(align_bam)
summary_info = self._parser.get_summary_metrics(align_metrics,
dup_metrics, insert_metrics, hybrid_metrics,
vrn_vals)
graphs = []
if gc_graph and os.path.exists(gc_graph):
graphs.append((gc_graph, "Distribution of GC content across reads"))
if insert_graph and os.path.exists(insert_graph):
graphs.append((insert_graph, "Distribution of paired end insert sizes"))
return summary_info, graphs |
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{'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'dup_metrics'}; {'id': '18', 'type': 'call', 'children': ['19', '22']}; {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': '_get_current_dup_metrics'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}; {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'align_metrics'}; {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'}; 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{'id': '46', 'type': 'assignment', 'children': ['47', '50']}; {'id': '47', 'type': 'pattern_list', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'insert_graph'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'insert_metrics'}; {'id': '50', 'type': 'call', 'children': ['51', '54']}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': '_insert_sizes'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}; {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'rnaseq_metrics'}; {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': '_rnaseq_metrics'}; {'id': '63', 'type': 'argument_list', 'children': ['64', '65', '66']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'gtf_file'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'rrna_file'}; {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'summary_info'}; {'id': '70', 'type': 'call', 'children': ['71', '76']}; {'id': '71', 'type': 'attribute', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': '_parser'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'get_summary_metrics'}; {'id': '76', 'type': 'argument_list', 'children': ['77', '78', '79', '82']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'align_metrics'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'dup_metrics'}; {'id': '79', 'type': 'keyword_argument', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'insert_metrics'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'insert_metrics'}; {'id': '82', 'type': 'keyword_argument', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'rnaseq_metrics'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'rnaseq_metrics'}; {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'graphs'}; {'id': '88', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '89', 'type': 'if_statement', 'children': ['90', '96']}; {'id': '90', 'type': 'boolean_operator', 'children': ['91', '92'], 'value': 'and'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'insert_graph'}; {'id': '92', 'type': 'call', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'insert_graph'}; {'id': '96', 'type': 'block', 'children': ['97']}; {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'call', 'children': ['99', '102']}; {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'graphs'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'tuple', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'insert_graph'}; {'id': '105', 'type': 'string', 'children': [], 'value': '"Distribution of paired end insert sizes"'}; {'id': '106', 'type': 'return_statement', 'children': ['107']}; {'id': '107', 'type': 'expression_list', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'summary_info'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'graphs'} | def report(self, align_bam, ref_file, gtf_file, is_paired=False, rrna_file="null"):
dup_metrics = self._get_current_dup_metrics(align_bam)
align_metrics = self._collect_align_metrics(align_bam, ref_file)
insert_graph, insert_metrics = (None, None)
if is_paired:
insert_graph, insert_metrics = self._insert_sizes(align_bam)
rnaseq_metrics = self._rnaseq_metrics(align_bam, gtf_file, rrna_file)
summary_info = self._parser.get_summary_metrics(align_metrics,
dup_metrics,
insert_metrics=insert_metrics,
rnaseq_metrics=rnaseq_metrics)
graphs = []
if insert_graph and file_exists(insert_graph):
graphs.append((insert_graph,
"Distribution of paired end insert sizes"))
return summary_info, graphs |
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{'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'get_recalibrate'}; {'id': '80', 'type': 'argument_list', 'children': ['81']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '82', 'type': 'string', 'children': [], 'value': '"sentieon"'}; {'id': '83', 'type': 'block', 'children': ['84']}; {'id': '84', 'type': 'if_statement', 'children': ['85', '91']}; {'id': '85', 'type': 'call', 'children': ['86', '89']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'string', 'children': [], 'value': '"prep_recal"'}; {'id': '91', 'type': 'block', 'children': ['92', '109']}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}; {'id': '93', 'type': 'call', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'binary_operator', 'children': ['99', '100'], 'value': '%'}; {'id': '99', 'type': 'string', 'children': [], 'value': '"Applying BQSR recalibration with sentieon: %s "'}; {'id': '100', 'type': 'call', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'get_sample_name'}; {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '114']}; {'id': '111', 'type': 'subscript', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '113', 'type': 'string', 'children': [], 'value': '"work_bam"'}; {'id': '114', 'type': 'call', 'children': ['115', '118']}; {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'sentieon'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'apply_bqsr'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '120', 'type': 'elif_clause', 'children': ['121', '127']}; {'id': '121', 'type': 'call', 'children': ['122', '125']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}; 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{'id': '138', 'type': 'identifier', 'children': [], 'value': 'get_recalibrate'}; {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '141', 'type': 'if_statement', 'children': ['142', '151']}; {'id': '142', 'type': 'boolean_operator', 'children': ['143', '145'], 'value': 'and'}; {'id': '143', 'type': 'not_operator', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'had_work_bam'}; {'id': '145', 'type': 'call', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'get_work_bam'}; {'id': '149', 'type': 'argument_list', 'children': ['150']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '151', 'type': 'block', 'children': ['152']}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}; 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{'id': '168', 'type': 'attribute', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'get_work_bam'}; {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': '!='}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'orig_bam'}; {'id': '175', 'type': 'call', 'children': ['176', '179']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'get_align_bam'}; {'id': '179', 'type': 'argument_list', 'children': ['180']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '181', 'type': 'block', 'children': ['182']}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}; {'id': '183', 'type': 'call', 'children': ['184', '187']}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'save_diskspace'}; {'id': '187', 'type': 'argument_list', 'children': ['188', '189', '197']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'orig_bam'}; {'id': '189', 'type': 'binary_operator', 'children': ['190', '191'], 'value': '%'}; {'id': '190', 'type': 'string', 'children': [], 'value': '"BAM recalibrated to %s"'}; {'id': '191', 'type': 'call', 'children': ['192', '195']}; {'id': '192', 'type': 'attribute', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'get_work_bam'}; {'id': '195', 'type': 'argument_list', 'children': ['196']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '197', 'type': 'subscript', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '199', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '200', 'type': 'return_statement', 'children': ['201']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'data'} | def apply_recal(data):
orig_bam = dd.get_align_bam(data) or dd.get_work_bam(data)
had_work_bam = "work_bam" in data
if dd.get_recalibrate(data) in [True, "gatk"]:
if data.get("prep_recal"):
logger.info("Applying BQSR recalibration with GATK: %s " % str(dd.get_sample_name(data)))
data["work_bam"] = _gatk_apply_bqsr(data)
elif dd.get_recalibrate(data) == "sentieon":
if data.get("prep_recal"):
logger.info("Applying BQSR recalibration with sentieon: %s " % str(dd.get_sample_name(data)))
data["work_bam"] = sentieon.apply_bqsr(data)
elif dd.get_recalibrate(data):
raise NotImplementedError("Unsupported recalibration type: %s" % (dd.get_recalibrate(data)))
if not had_work_bam and dd.get_work_bam(data):
data["align_bam"] = dd.get_work_bam(data)
if orig_bam != dd.get_work_bam(data) and orig_bam != dd.get_align_bam(data):
utils.save_diskspace(orig_bam, "BAM recalibrated to %s" % dd.get_work_bam(data), data["config"])
return data |
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{'id': '15', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '18', 'type': 'argument_list', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'work_dir'}; {'id': '20', 'type': 'binary_operator', 'children': ['21', '22'], 'value': '%'}; {'id': '21', 'type': 'string', 'children': [], 'value': '"%s-merge.bed.gz"'}; {'id': '22', 'type': 'subscript', 'children': ['23', '36']}; {'id': '23', 'type': 'call', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'call', 'children': ['29', '34']}; {'id': '29', 'type': 'attribute', 'children': ['30', '33']}; 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{'id': '46', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '47', 'type': 'if_statement', 'children': ['48', '56']}; {'id': '48', 'type': 'not_operator', 'children': ['49']}; {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'file_uptodate'}; {'id': '53', 'type': 'argument_list', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '56', 'type': 'block', 'children': ['57']}; {'id': '57', 'type': 'with_statement', 'children': ['58', '68']}; {'id': '58', 'type': 'with_clause', 'children': ['59']}; {'id': '59', 'type': 'with_item', 'children': ['60']}; {'id': '60', 'type': 'as_pattern', 'children': ['61', '66']}; {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '63', 'type': 'argument_list', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '66', 'type': 'as_pattern_target', 'children': ['67']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '68', 'type': 'block', 'children': ['69', '83', '90']}; {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'fai_file'}; {'id': '72', 'type': 'call', 'children': ['73', '76']}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'fasta_idx'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}; {'id': '77', 'type': 'call', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'get_ref_file'}; {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '86', 'type': '()', 'children': ['87']}; {'id': '87', 'type': 'concatenated_string', 'children': ['88', '89']}; {'id': '88', 'type': 'string', 'children': [], 'value': '"{gsort} {in_file} {fai_file} | bedtools merge -i - -d {stats[merge_size]} | "'}; {'id': '89', 'type': 'string', 'children': [], 'value': '"bgzip -c > {tx_out_file}"'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}; {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'do'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '95', 'type': 'argument_list', 'children': ['96', '105']}; {'id': '96', 'type': 'call', 'children': ['97', '100']}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}; {'id': '101', 'type': 'dictionary_splat', 'children': ['102']}; {'id': '102', 'type': 'call', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '104', 'type': 'argument_list', 'children': []}; {'id': '105', 'type': 'string', 'children': [], 'value': '"Prepare SV callable BED regions"'}; {'id': '106', 'type': 'return_statement', 'children': ['107']}; {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'vcfutils'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'bgzip_and_index'}; {'id': '111', 'type': 'argument_list', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '113', 'type': 'subscript', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '115', 'type': 'string', 'children': [], 'value': '"config"'} | def _prep_callable_bed(in_file, work_dir, stats, data):
out_file = os.path.join(work_dir, "%s-merge.bed.gz" % utils.splitext_plus(os.path.basename(in_file))[0])
gsort = config_utils.get_program("gsort", data)
if not utils.file_uptodate(out_file, in_file):
with file_transaction(data, out_file) as tx_out_file:
fai_file = ref.fasta_idx(dd.get_ref_file(data))
cmd = ("{gsort} {in_file} {fai_file} | bedtools merge -i - -d {stats[merge_size]} | "
"bgzip -c > {tx_out_file}")
do.run(cmd.format(**locals()), "Prepare SV callable BED regions")
return vcfutils.bgzip_and_index(out_file, data["config"]) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'fake_index'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '6', 'type': 'block', 'children': ['7', '13', '53']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'index_file'}; {'id': '10', 'type': 'binary_operator', 'children': ['11', '12'], 'value': '%'}; {'id': '11', 'type': 'string', 'children': [], 'value': '"%s.bai"'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '13', 'type': 'if_statement', 'children': ['14', '21']}; {'id': '14', 'type': 'not_operator', 'children': ['15']}; {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'index_file'}; {'id': '21', 'type': 'block', 'children': ['22']}; {'id': '22', 'type': 'with_statement', 'children': ['23', '33']}; {'id': '23', 'type': 'with_clause', 'children': ['24']}; {'id': '24', 'type': 'with_item', 'children': ['25']}; {'id': '25', 'type': 'as_pattern', 'children': ['26', '31']}; {'id': '26', 'type': 'call', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'index_file'}; {'id': '31', 'type': 'as_pattern_target', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '33', 'type': 'block', 'children': ['34']}; {'id': '34', 'type': 'with_statement', 'children': ['35', '45']}; {'id': '35', 'type': 'with_clause', 'children': ['36']}; {'id': '36', 'type': 'with_item', 'children': ['37']}; {'id': '37', 'type': 'as_pattern', 'children': ['38', '43']}; {'id': '38', 'type': 'call', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '40', 'type': 'argument_list', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '42', 'type': 'string', 'children': [], 'value': '"w"'}; {'id': '43', 'type': 'as_pattern_target', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '45', 'type': 'block', 'children': ['46']}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'string', 'children': [], 'value': '"name sorted -- no index"'}; {'id': '53', 'type': 'return_statement', 'children': ['54']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'index_file'} | def fake_index(in_bam, data):
index_file = "%s.bai" % in_bam
if not utils.file_exists(index_file):
with file_transaction(data, index_file) as tx_out_file:
with open(tx_out_file, "w") as out_handle:
out_handle.write("name sorted -- no index")
return index_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'order'}; {'id': '8', 'type': 'string', 'children': [], 'value': '"coordinate"'}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'out_dir'}; {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'block', 'children': ['13', '21', '31', '40', '46', '203']}; {'id': '13', 'type': 'assert_statement', 'children': ['14', '18']}; {'id': '14', 'type': 'call', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'is_bam'}; {'id': '16', 'type': 'argument_list', 'children': ['17']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '18', 'type': 'binary_operator', 'children': ['19', '20'], 'value': '%'}; {'id': '19', 'type': 'string', 'children': [], 'value': '"%s in not a BAM file"'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '21', 'type': 'if_statement', 'children': ['22', '28']}; {'id': '22', 'type': 'call', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'bam_already_sorted'}; {'id': '24', 'type': 'argument_list', 'children': ['25', '26', '27']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'order'}; {'id': '28', 'type': 'block', 'children': ['29']}; {'id': '29', 'type': 'return_statement', 'children': ['30']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'sort_stem'}; {'id': '34', 'type': 'call', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': '_get_sort_stem'}; {'id': '36', 'type': 'argument_list', 'children': ['37', '38', '39']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'order'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'out_dir'}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'sort_file'}; {'id': '43', 'type': 'binary_operator', 'children': ['44', '45'], 'value': '+'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'sort_stem'}; {'id': '45', 'type': 'string', 'children': [], 'value': '".bam"'}; {'id': '46', 'type': 'if_statement', 'children': ['47', '54']}; {'id': '47', 'type': 'not_operator', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '52']}; {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'sort_file'}; {'id': '54', 'type': 'block', 'children': ['55', '65', '77']}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'samtools'}; {'id': '58', 'type': 'call', 'children': ['59', '62']}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'get_program'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '64']}; {'id': '63', 'type': 'string', 'children': [], 'value': '"samtools"'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'cores'}; {'id': '68', 'type': 'call', 'children': ['69', '74']}; {'id': '69', 'type': 'attribute', 'children': ['70', '73']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '72', 'type': 'string', 'children': [], 'value': '"algorithm"'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '74', 'type': 'argument_list', 'children': ['75', '76']}; {'id': '75', 'type': 'string', 'children': [], 'value': '"num_cores"'}; {'id': '76', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '77', 'type': 'with_statement', 'children': ['78', '88']}; {'id': '78', 'type': 'with_clause', 'children': ['79']}; {'id': '79', 'type': 'with_item', 'children': ['80']}; {'id': '80', 'type': 'as_pattern', 'children': ['81', '86']}; {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '83', 'type': 'argument_list', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'sort_file'}; {'id': '86', 'type': 'as_pattern_target', 'children': ['87']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'tx_sort_file'}; {'id': '88', 'type': 'block', 'children': ['89', '102', '118', '127', '137', '161', '168']}; {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'assignment', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'tx_sort_stem'}; {'id': '92', 'type': 'subscript', 'children': ['93', '101']}; {'id': '93', 'type': 'call', 'children': ['94', '99']}; {'id': '94', 'type': 'attribute', 'children': ['95', '98']}; {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'splitext'}; {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'tx_sort_file'}; {'id': '101', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'tx_dir'}; {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'safe_makedir'}; {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'call', 'children': ['111', '116']}; {'id': '111', 'type': 'attribute', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'dirname'}; {'id': '116', 'type': 'argument_list', 'children': ['117']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'tx_sort_file'}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}; {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'order_flag'}; {'id': '121', 'type': 'conditional_expression', 'children': ['122', '123', '126'], 'value': 'if'}; {'id': '122', 'type': 'string', 'children': [], 'value': '"-n"'}; {'id': '123', 'type': 'comparison_operator', 'children': ['124', '125'], 'value': '=='}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'order'}; {'id': '125', 'type': 'string', 'children': [], 'value': '"queryname"'}; {'id': '126', 'type': 'string', 'children': [], 'value': '""'}; {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'assignment', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'resources'}; {'id': '130', 'type': 'call', 'children': ['131', '134']}; {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'get_resources'}; {'id': '134', 'type': 'argument_list', 'children': ['135', '136']}; {'id': '135', 'type': 'string', 'children': [], 'value': '"samtools"'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'assignment', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'mem'}; {'id': '140', 'type': 'call', 'children': ['141', '160']}; {'id': '141', 'type': 'attribute', 'children': ['142', '159']}; {'id': '142', 'type': 'call', 'children': ['143', '146']}; {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'adjust_memory'}; {'id': '146', 'type': 'argument_list', 'children': ['147', '154', '155', '156']}; {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'resources'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '151', 'type': 'argument_list', 'children': ['152', '153']}; {'id': '152', 'type': 'string', 'children': [], 'value': '"memory"'}; {'id': '153', 'type': 'string', 'children': [], 'value': '"2G"'}; {'id': '154', 'type': 'float', 'children': [], 'value': '1.25'}; {'id': '155', 'type': 'string', 'children': [], 'value': '"decrease"'}; {'id': '156', 'type': 'keyword_argument', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'out_modifier'}; {'id': '158', 'type': 'string', 'children': [], 'value': '"M"'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '160', 'type': 'argument_list', 'children': []}; {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'assignment', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '164', 'type': '()', 'children': ['165']}; {'id': '165', 'type': 'concatenated_string', 'children': ['166', '167']}; {'id': '166', 'type': 'string', 'children': [], 'value': '"{samtools} sort -@ {cores} -m {mem} -O BAM {order_flag} "'}; {'id': '167', 'type': 'string', 'children': [], 'value': '"-T {tx_sort_stem}-sort -o {tx_sort_file} {in_bam}"'}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}; {'id': '169', 'type': 'call', 'children': ['170', '173']}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'do'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '173', 'type': 'argument_list', 'children': ['174', '183']}; {'id': '174', 'type': 'call', 'children': ['175', '178']}; {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}; {'id': '179', 'type': 'dictionary_splat', 'children': ['180']}; {'id': '180', 'type': 'call', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '182', 'type': 'argument_list', 'children': []}; {'id': '183', 'type': 'binary_operator', 'children': ['184', '185'], 'value': '%'}; {'id': '184', 'type': 'string', 'children': [], 'value': '"Sort BAM file %s: %s to %s"'}; {'id': '185', 'type': 'tuple', 'children': ['186', '187', '195']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'order'}; {'id': '187', 'type': 'call', 'children': ['188', '193']}; {'id': '188', 'type': 'attribute', 'children': ['189', '192']}; {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '193', 'type': 'argument_list', 'children': ['194']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '195', 'type': 'call', 'children': ['196', '201']}; {'id': '196', 'type': 'attribute', 'children': ['197', '200']}; {'id': '197', 'type': 'attribute', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'sort_file'}; {'id': '203', 'type': 'return_statement', 'children': ['204']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'sort_file'} | def sort(in_bam, config, order="coordinate", out_dir=None):
assert is_bam(in_bam), "%s in not a BAM file" % in_bam
if bam_already_sorted(in_bam, config, order):
return in_bam
sort_stem = _get_sort_stem(in_bam, order, out_dir)
sort_file = sort_stem + ".bam"
if not utils.file_exists(sort_file):
samtools = config_utils.get_program("samtools", config)
cores = config["algorithm"].get("num_cores", 1)
with file_transaction(config, sort_file) as tx_sort_file:
tx_sort_stem = os.path.splitext(tx_sort_file)[0]
tx_dir = utils.safe_makedir(os.path.dirname(tx_sort_file))
order_flag = "-n" if order == "queryname" else ""
resources = config_utils.get_resources("samtools", config)
mem = config_utils.adjust_memory(resources.get("memory", "2G"),
1.25, "decrease", out_modifier="M").upper()
cmd = ("{samtools} sort -@ {cores} -m {mem} -O BAM {order_flag} "
"-T {tx_sort_stem}-sort -o {tx_sort_file} {in_bam}")
do.run(cmd.format(**locals()), "Sort BAM file %s: %s to %s" %
(order, os.path.basename(in_bam), os.path.basename(sort_file)))
return sort_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'tobam_cl'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'is_paired'}; {'id': '8', 'type': 'False', 'children': []}; {'id': '9', 'type': 'block', 'children': ['10', '17', '26']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}; {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'do_dedup'}; {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': '_check_dedup'}; {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'umi_consensus'}; {'id': '20', 'type': 'call', 'children': ['21', '24']}; {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'get_umi_consensus'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '26', 'type': 'with_statement', 'children': ['27', '37']}; {'id': '27', 'type': 'with_clause', 'children': ['28']}; {'id': '28', 'type': 'with_item', 'children': ['29']}; {'id': '29', 'type': 'as_pattern', 'children': ['30', '35']}; {'id': '30', 'type': 'call', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '35', 'type': 'as_pattern_target', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '37', 'type': 'block', 'children': ['38']}; {'id': '38', 'type': 'if_statement', 'children': ['39', '41', '51', '64', '148']}; {'id': '39', 'type': 'not_operator', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'do_dedup'}; {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'yield', 'children': ['44']}; {'id': '44', 'type': 'tuple', 'children': ['45', '50']}; {'id': '45', 'type': 'call', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'sam_to_sortbam_cl'}; {'id': '47', 'type': 'argument_list', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '51', 'type': 'elif_clause', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'umi_consensus'}; {'id': '53', 'type': 'block', 'children': ['54']}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}; {'id': '55', 'type': 'yield', 'children': ['56']}; {'id': '56', 'type': 'tuple', 'children': ['57', '63']}; {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': '_sam_to_grouped_umi_cl'}; {'id': '59', 'type': 'argument_list', 'children': ['60', '61', '62']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'umi_consensus'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '64', 'type': 'elif_clause', 'children': ['65', '82']}; {'id': '65', 'type': 'boolean_operator', 'children': ['66', '72'], 'value': 'and'}; {'id': '66', 'type': 'boolean_operator', 'children': ['67', '68'], 'value': 'and'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'is_paired'}; {'id': '68', 'type': 'call', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': '_need_sr_disc_reads'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '72', 'type': 'not_operator', 'children': ['73']}; {'id': '73', 'type': 'call', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': '_too_many_contigs'}; {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'call', 'children': ['77', '80']}; {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'get_ref_file'}; {'id': '80', 'type': 'argument_list', 'children': ['81']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '82', 'type': 'block', 'children': ['83', '98', '113']}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'sr_file'}; {'id': '86', 'type': 'binary_operator', 'children': ['87', '88'], 'value': '%'}; {'id': '87', 'type': 'string', 'children': [], 'value': '"%s-sr.bam"'}; {'id': '88', 'type': 'subscript', 'children': ['89', '97']}; {'id': '89', 'type': 'call', 'children': ['90', '95']}; {'id': '90', 'type': 'attribute', 'children': ['91', '94']}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'splitext'}; {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '97', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}; {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'disc_file'}; {'id': '101', 'type': 'binary_operator', 'children': ['102', '103'], 'value': '%'}; {'id': '102', 'type': 'string', 'children': [], 'value': '"%s-disc.bam"'}; {'id': '103', 'type': 'subscript', 'children': ['104', '112']}; {'id': '104', 'type': 'call', 'children': ['105', '110']}; {'id': '105', 'type': 'attribute', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'splitext'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '112', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '113', 'type': 'with_statement', 'children': ['114', '124']}; {'id': '114', 'type': 'with_clause', 'children': ['115']}; {'id': '115', 'type': 'with_item', 'children': ['116']}; {'id': '116', 'type': 'as_pattern', 'children': ['117', '122']}; {'id': '117', 'type': 'call', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '119', 'type': 'argument_list', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'sr_file'}; {'id': '122', 'type': 'as_pattern_target', 'children': ['123']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'tx_sr_file'}; {'id': '124', 'type': 'block', 'children': ['125']}; {'id': '125', 'type': 'with_statement', 'children': ['126', '136']}; {'id': '126', 'type': 'with_clause', 'children': ['127']}; {'id': '127', 'type': 'with_item', 'children': ['128']}; {'id': '128', 'type': 'as_pattern', 'children': ['129', '134']}; {'id': '129', 'type': 'call', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '131', 'type': 'argument_list', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'disc_file'}; {'id': '134', 'type': 'as_pattern_target', 'children': ['135']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'tx_disc_file'}; {'id': '136', 'type': 'block', 'children': ['137']}; {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'yield', 'children': ['139']}; {'id': '139', 'type': 'tuple', 'children': ['140', '147']}; {'id': '140', 'type': 'call', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'samblaster_dedup_sort'}; {'id': '142', 'type': 'argument_list', 'children': ['143', '144', '145', '146']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'tx_sr_file'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'tx_disc_file'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '148', 'type': 'else_clause', 'children': ['149']}; {'id': '149', 'type': 'block', 'children': ['150']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}; {'id': '151', 'type': 'yield', 'children': ['152']}; {'id': '152', 'type': 'tuple', 'children': ['153', '158']}; {'id': '153', 'type': 'call', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': '_biobambam_dedup_sort'}; {'id': '155', 'type': 'argument_list', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'} | def tobam_cl(data, out_file, is_paired=False):
do_dedup = _check_dedup(data)
umi_consensus = dd.get_umi_consensus(data)
with file_transaction(data, out_file) as tx_out_file:
if not do_dedup:
yield (sam_to_sortbam_cl(data, tx_out_file), tx_out_file)
elif umi_consensus:
yield (_sam_to_grouped_umi_cl(data, umi_consensus, tx_out_file), tx_out_file)
elif is_paired and _need_sr_disc_reads(data) and not _too_many_contigs(dd.get_ref_file(data)):
sr_file = "%s-sr.bam" % os.path.splitext(out_file)[0]
disc_file = "%s-disc.bam" % os.path.splitext(out_file)[0]
with file_transaction(data, sr_file) as tx_sr_file:
with file_transaction(data, disc_file) as tx_disc_file:
yield (samblaster_dedup_sort(data, tx_out_file, tx_sr_file, tx_disc_file),
tx_out_file)
else:
yield (_biobambam_dedup_sort(data, tx_out_file), tx_out_file) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sam_to_sortbam_cl'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'name_sort'}; {'id': '8', 'type': 'False', 'children': []}; {'id': '9', 'type': 'block', 'children': ['10', '22', '34', '47', '54']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}; {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'samtools'}; {'id': '13', 'type': 'call', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'get_program'}; {'id': '17', 'type': 'argument_list', 'children': ['18', '19']}; {'id': '18', 'type': 'string', 'children': [], 'value': '"samtools"'}; {'id': '19', 'type': 'subscript', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '21', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '27']}; {'id': '24', 'type': 'pattern_list', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'cores'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'mem'}; {'id': '27', 'type': 'call', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': '_get_cores_memory'}; {'id': '29', 'type': 'argument_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '31', 'type': 'keyword_argument', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'downscale'}; {'id': '33', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}; {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'tmp_file'}; {'id': '37', 'type': 'binary_operator', 'children': ['38', '39'], 'value': '%'}; {'id': '38', 'type': 'string', 'children': [], 'value': '"%s-sorttmp"'}; {'id': '39', 'type': 'subscript', 'children': ['40', '46']}; {'id': '40', 'type': 'call', 'children': ['41', '44']}; {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '46', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'sort_flag'}; {'id': '50', 'type': 'conditional_expression', 'children': ['51', '52', '53'], 'value': 'if'}; {'id': '51', 'type': 'string', 'children': [], 'value': '"-n"'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'name_sort'}; {'id': '53', 'type': 'string', 'children': [], 'value': '""'}; {'id': '54', 'type': 'return_statement', 'children': ['55']}; {'id': '55', 'type': '()', 'children': ['56']}; {'id': '56', 'type': 'call', 'children': ['57', '62']}; {'id': '57', 'type': 'attribute', 'children': ['58', '61']}; {'id': '58', 'type': 'concatenated_string', 'children': ['59', '60']}; {'id': '59', 'type': 'string', 'children': [], 'value': '"{samtools} sort -@ {cores} -m {mem} {sort_flag} "'}; {'id': '60', 'type': 'string', 'children': [], 'value': '"-T {tmp_file} -o {tx_out_file} /dev/stdin"'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}; {'id': '63', 'type': 'dictionary_splat', 'children': ['64']}; {'id': '64', 'type': 'call', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '66', 'type': 'argument_list', 'children': []} | def sam_to_sortbam_cl(data, tx_out_file, name_sort=False):
samtools = config_utils.get_program("samtools", data["config"])
cores, mem = _get_cores_memory(data, downscale=2)
tmp_file = "%s-sorttmp" % utils.splitext_plus(tx_out_file)[0]
sort_flag = "-n" if name_sort else ""
return ("{samtools} sort -@ {cores} -m {mem} {sort_flag} "
"-T {tmp_file} -o {tx_out_file} /dev/stdin".format(**locals())) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'samblaster_dedup_sort'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'tx_sr_file'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'tx_disc_file'}; {'id': '8', 'type': 'block', 'children': ['9', '21', '33', '46', '51', '63', '81', '100', '148', '152', '164', '184', '204', '211']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'samblaster'}; {'id': '12', 'type': 'call', 'children': ['13', '16']}; {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; 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{'id': '29', 'type': 'string', 'children': [], 'value': '"samtools"'}; {'id': '30', 'type': 'subscript', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '32', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'tmp_prefix'}; {'id': '36', 'type': 'binary_operator', 'children': ['37', '38'], 'value': '%'}; {'id': '37', 'type': 'string', 'children': [], 'value': '"%s-sorttmp"'}; {'id': '38', 'type': 'subscript', 'children': ['39', '45']}; {'id': '39', 'type': 'call', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '45', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'tobam_cmd'}; {'id': '49', 'type': '()', 'children': ['50']}; {'id': '50', 'type': 'string', 'children': [], 'value': '"{samtools} sort {sort_opt} -@ {cores} -m {mem} -T {tmp_prefix}-{dext} {out_file} -"'}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '56']}; {'id': '53', 'type': 'pattern_list', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'cores'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'mem'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': '_get_cores_memory'}; {'id': '58', 'type': 'argument_list', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '60', 'type': 'keyword_argument', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'downscale'}; {'id': '62', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'ds_cmd'}; {'id': '66', 'type': 'conditional_expression', 'children': ['67', '68', '74'], 'value': 'if'}; {'id': '67', 'type': 'None', 'children': []}; {'id': '68', 'type': 'call', 'children': ['69', '72']}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '72', 'type': 'argument_list', 'children': ['73']}; {'id': '73', 'type': 'string', 'children': [], 'value': '"align_split"'}; {'id': '74', 'type': 'call', 'children': ['75', '78']}; {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'bam'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'get_maxcov_downsample_cl'}; {'id': '78', 'type': 'argument_list', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '80', 'type': 'string', 'children': [], 'value': '"samtools"'}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'sort_opt'}; {'id': '84', 'type': 'conditional_expression', 'children': ['85', '86', '99'], 'value': 'if'}; {'id': '85', 'type': 'string', 'children': [], 'value': '"-n"'}; {'id': '86', 'type': 'boolean_operator', 'children': ['87', '93'], 'value': 'and'}; {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'string', 'children': [], 'value': '"align_split"'}; {'id': '93', 'type': 'call', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'get_mark_duplicates'}; {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '99', 'type': 'string', 'children': [], 'value': '""'}; {'id': '100', 'type': 'if_statement', 'children': ['101', '102', '126']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'ds_cmd'}; {'id': '102', 'type': 'block', 'children': ['103']}; {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'dedup_cmd'}; {'id': '106', 'type': 'binary_operator', 'children': ['107', '108'], 'value': '%'}; {'id': '107', 'type': 'string', 'children': [], 'value': '"%s %s > %s"'}; {'id': '108', 'type': 'tuple', 'children': ['109', '124', '125']}; {'id': '109', 'type': 'call', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'tobam_cmd'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '113', 'type': 'argument_list', 'children': ['114', '117', '120']}; {'id': '114', 'type': 'keyword_argument', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '116', 'type': 'string', 'children': [], 'value': '""'}; {'id': '117', 'type': 'keyword_argument', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'dext'}; {'id': '119', 'type': 'string', 'children': [], 'value': '"full"'}; {'id': '120', 'type': 'dictionary_splat', 'children': ['121']}; {'id': '121', 'type': 'call', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '123', 'type': 'argument_list', 'children': []}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'ds_cmd'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '126', 'type': 'else_clause', 'children': ['127']}; {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}; {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'dedup_cmd'}; {'id': '131', 'type': 'call', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'tobam_cmd'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '135', 'type': 'argument_list', 'children': ['136', '141', '144']}; {'id': '136', 'type': 'keyword_argument', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '138', 'type': 'binary_operator', 'children': ['139', '140'], 'value': '%'}; {'id': '139', 'type': 'string', 'children': [], 'value': '"-o %s"'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '141', 'type': 'keyword_argument', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'dext'}; {'id': '143', 'type': 'string', 'children': [], 'value': '"full"'}; {'id': '144', 'type': 'dictionary_splat', 'children': ['145']}; {'id': '145', 'type': 'call', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '147', 'type': 'argument_list', 'children': []}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}; {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'sort_opt'}; {'id': '151', 'type': 'string', 'children': [], 'value': '""'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}; {'id': '153', 'type': 'assignment', 'children': ['154', '157']}; {'id': '154', 'type': 'pattern_list', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'cores'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'mem'}; {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': '_get_cores_memory'}; {'id': '159', 'type': 'argument_list', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '161', 'type': 'keyword_argument', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'downscale'}; {'id': '163', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}; {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'splitter_cmd'}; {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'tobam_cmd'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '171', 'type': 'argument_list', 'children': ['172', '177', '180']}; {'id': '172', 'type': 'keyword_argument', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '174', 'type': 'binary_operator', 'children': ['175', '176'], 'value': '%'}; {'id': '175', 'type': 'string', 'children': [], 'value': '"-o %s"'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'tx_sr_file'}; {'id': '177', 'type': 'keyword_argument', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'dext'}; {'id': '179', 'type': 'string', 'children': [], 'value': '"spl"'}; {'id': '180', 'type': 'dictionary_splat', 'children': ['181']}; {'id': '181', 'type': 'call', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '183', 'type': 'argument_list', 'children': []}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}; {'id': '185', 'type': 'assignment', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'discordant_cmd'}; {'id': '187', 'type': 'call', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'tobam_cmd'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '191', 'type': 'argument_list', 'children': ['192', '197', '200']}; {'id': '192', 'type': 'keyword_argument', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '194', 'type': 'binary_operator', 'children': ['195', '196'], 'value': '%'}; {'id': '195', 'type': 'string', 'children': [], 'value': '"-o %s"'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'tx_disc_file'}; {'id': '197', 'type': 'keyword_argument', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'dext'}; {'id': '199', 'type': 'string', 'children': [], 'value': '"disc"'}; {'id': '200', 'type': 'dictionary_splat', 'children': ['201']}; {'id': '201', 'type': 'call', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '203', 'type': 'argument_list', 'children': []}; {'id': '204', 'type': 'expression_statement', 'children': ['205']}; {'id': '205', 'type': 'assignment', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '207', 'type': '()', 'children': ['208']}; {'id': '208', 'type': 'concatenated_string', 'children': ['209', '210']}; {'id': '209', 'type': 'string', 'children': [], 'value': '"{samblaster} --addMateTags -M --splitterFile >({splitter_cmd}) --discordantFile >({discordant_cmd}) "'}; {'id': '210', 'type': 'string', 'children': [], 'value': '"| {dedup_cmd}"'}; {'id': '211', 'type': 'return_statement', 'children': ['212']}; {'id': '212', 'type': 'call', 'children': ['213', '216']}; {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '216', 'type': 'argument_list', 'children': ['217']}; {'id': '217', 'type': 'dictionary_splat', 'children': ['218']}; {'id': '218', 'type': 'call', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '220', 'type': 'argument_list', 'children': []} | def samblaster_dedup_sort(data, tx_out_file, tx_sr_file, tx_disc_file):
samblaster = config_utils.get_program("samblaster", data["config"])
samtools = config_utils.get_program("samtools", data["config"])
tmp_prefix = "%s-sorttmp" % utils.splitext_plus(tx_out_file)[0]
tobam_cmd = ("{samtools} sort {sort_opt} -@ {cores} -m {mem} -T {tmp_prefix}-{dext} {out_file} -")
cores, mem = _get_cores_memory(data, downscale=2)
ds_cmd = None if data.get("align_split") else bam.get_maxcov_downsample_cl(data, "samtools")
sort_opt = "-n" if data.get("align_split") and dd.get_mark_duplicates(data) else ""
if ds_cmd:
dedup_cmd = "%s %s > %s" % (tobam_cmd.format(out_file="", dext="full", **locals()), ds_cmd, tx_out_file)
else:
dedup_cmd = tobam_cmd.format(out_file="-o %s" % tx_out_file, dext="full", **locals())
sort_opt = ""
cores, mem = _get_cores_memory(data, downscale=4)
splitter_cmd = tobam_cmd.format(out_file="-o %s" % tx_sr_file, dext="spl", **locals())
discordant_cmd = tobam_cmd.format(out_file="-o %s" % tx_disc_file, dext="disc", **locals())
cmd = ("{samblaster} --addMateTags -M --splitterFile >({splitter_cmd}) --discordantFile >({discordant_cmd}) "
"| {dedup_cmd}")
return cmd.format(**locals()) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_biobambam_dedup_sort'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '6', 'type': 'block', 'children': ['7', '19', '31', '44', '124']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'samtools'}; {'id': '10', 'type': 'call', 'children': ['11', '14']}; {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'get_program'}; {'id': '14', 'type': 'argument_list', 'children': ['15', '16']}; {'id': '15', 'type': 'string', 'children': [], 'value': '"samtools"'}; {'id': '16', 'type': 'subscript', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '18', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '24']}; {'id': '21', 'type': 'pattern_list', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'cores'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'mem'}; {'id': '24', 'type': 'call', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': '_get_cores_memory'}; {'id': '26', 'type': 'argument_list', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '28', 'type': 'keyword_argument', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'downscale'}; {'id': '30', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'tmp_file'}; {'id': '34', 'type': 'binary_operator', 'children': ['35', '36'], 'value': '%'}; {'id': '35', 'type': 'string', 'children': [], 'value': '"%s-sorttmp"'}; {'id': '36', 'type': 'subscript', 'children': ['37', '43']}; {'id': '37', 'type': 'call', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '43', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '44', 'type': 'if_statement', 'children': ['45', '51', '75']}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'string', 'children': [], 'value': '"align_split"'}; {'id': '51', 'type': 'block', 'children': ['52', '69']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}; {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'sort_opt'}; {'id': '55', 'type': 'conditional_expression', 'children': ['56', '57', '68'], 'value': 'if'}; {'id': '56', 'type': 'string', 'children': [], 'value': '"-n"'}; {'id': '57', 'type': 'boolean_operator', 'children': ['58', '64'], 'value': 'and'}; {'id': '58', 'type': 'call', 'children': ['59', '62']}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}; {'id': '63', 'type': 'string', 'children': [], 'value': '"align_split"'}; {'id': '64', 'type': 'call', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': '_check_dedup'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '68', 'type': 'string', 'children': [], 'value': '""'}; {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '72', 'type': 'binary_operator', 'children': ['73', '74'], 'value': '%'}; {'id': '73', 'type': 'string', 'children': [], 'value': '"{samtools} sort %s -@ {cores} -m {mem} -O bam -T {tmp_file}-namesort -o {tx_out_file} -"'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'sort_opt'}; {'id': '75', 'type': 'else_clause', 'children': ['76']}; {'id': '76', 'type': 'block', 'children': ['77', '95', '105', '115']}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'cores'}; {'id': '80', 'type': 'call', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '82', 'type': 'argument_list', 'children': ['83', '84']}; {'id': '83', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'math'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'ceil'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'binary_operator', 'children': ['93', '94'], 'value': '*'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'cores'}; {'id': '94', 'type': 'float', 'children': [], 'value': '0.75'}; {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'assignment', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'ds_cmd'}; {'id': '98', 'type': 'call', 'children': ['99', '102']}; {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'bam'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'get_maxcov_downsample_cl'}; {'id': '102', 'type': 'argument_list', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '104', 'type': 'string', 'children': [], 'value': '"bamsormadup"'}; {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'assignment', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'bamsormadup'}; {'id': '108', 'type': 'call', 'children': ['109', '112']}; {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'config_utils'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'get_program'}; {'id': '112', 'type': 'argument_list', 'children': ['113', '114']}; {'id': '113', 'type': 'string', 'children': [], 'value': '"bamsormadup"'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '118', 'type': '()', 'children': ['119']}; {'id': '119', 'type': 'binary_operator', 'children': ['120', '123'], 'value': '%'}; {'id': '120', 'type': 'concatenated_string', 'children': ['121', '122']}; {'id': '121', 'type': 'string', 'children': [], 'value': '"{bamsormadup} inputformat=sam threads={cores} tmpfile={tmp_file}-markdup "'}; {'id': '122', 'type': 'string', 'children': [], 'value': '"SO=coordinate %s > {tx_out_file}"'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'ds_cmd'}; {'id': '124', 'type': 'return_statement', 'children': ['125']}; {'id': '125', 'type': 'call', 'children': ['126', '129']}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '129', 'type': 'argument_list', 'children': ['130']}; {'id': '130', 'type': 'dictionary_splat', 'children': ['131']}; {'id': '131', 'type': 'call', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '133', 'type': 'argument_list', 'children': []} | def _biobambam_dedup_sort(data, tx_out_file):
samtools = config_utils.get_program("samtools", data["config"])
cores, mem = _get_cores_memory(data, downscale=2)
tmp_file = "%s-sorttmp" % utils.splitext_plus(tx_out_file)[0]
if data.get("align_split"):
sort_opt = "-n" if data.get("align_split") and _check_dedup(data) else ""
cmd = "{samtools} sort %s -@ {cores} -m {mem} -O bam -T {tmp_file}-namesort -o {tx_out_file} -" % sort_opt
else:
cores = max(1, int(math.ceil(cores * 0.75)))
ds_cmd = bam.get_maxcov_downsample_cl(data, "bamsormadup")
bamsormadup = config_utils.get_program("bamsormadup", data)
cmd = ("{bamsormadup} inputformat=sam threads={cores} tmpfile={tmp_file}-markdup "
"SO=coordinate %s > {tx_out_file}" % ds_cmd)
return cmd.format(**locals()) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_prepare_bam_file'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'bam_file'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '7', 'type': 'block', 'children': ['8', '16', '30']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'sort_mode'}; {'id': '11', 'type': 'call', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': '_get_sort_order'}; {'id': '13', 'type': 'argument_list', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'bam_file'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '16', 'type': 'if_statement', 'children': ['17', '20']}; {'id': '17', 'type': 'comparison_operator', 'children': ['18', '19'], 'value': '!='}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'sort_mode'}; {'id': '19', 'type': 'string', 'children': [], 'value': '"queryname"'}; {'id': '20', 'type': 'block', 'children': ['21']}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'bam_file'}; {'id': '24', 'type': 'call', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '26', 'type': 'argument_list', 'children': ['27', '28', '29']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'bam_file'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '29', 'type': 'string', 'children': [], 'value': '"queryname"'}; {'id': '30', 'type': 'return_statement', 'children': ['31']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'bam_file'} | def _prepare_bam_file(bam_file, tmp_dir, config):
sort_mode = _get_sort_order(bam_file, config)
if sort_mode != "queryname":
bam_file = sort(bam_file, config, "queryname")
return bam_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_concat_records'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'items_by_key'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'input_order'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '33', '42', '51', '99']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'all_records'}; {'id': '10', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '11', 'type': 'for_statement', 'children': ['12', '15', '20']}; {'id': '12', 'type': 'tuple_pattern', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'input_order'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '19', 'type': 'argument_list', 'children': []}; {'id': '20', 'type': 'block', 'children': ['21']}; {'id': '21', 'type': 'if_statement', 'children': ['22', '25']}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '24'], 'value': '=='}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '24', 'type': 'string', 'children': [], 'value': '"record"'}; {'id': '25', 'type': 'block', 'children': ['26']}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'all_records'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'out_items_by_key'}; {'id': '36', 'type': 'call', 'children': ['37', '40']}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'deepish_copy'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'items_by_key'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'out_input_order'}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'deepish_copy'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'input_order'}; {'id': '51', 'type': 'if_statement', 'children': ['52', '58']}; {'id': '52', 'type': 'comparison_operator', 'children': ['53', '57'], 'value': '>'}; {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'all_records'}; {'id': '57', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '58', 'type': 'block', 'children': ['59', '65', '71', '93']}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'final_k'}; {'id': '62', 'type': 'subscript', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'all_records'}; {'id': '64', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'final_v'}; {'id': '68', 'type': 'subscript', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'items_by_key'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'final_k'}; {'id': '71', 'type': 'for_statement', 'children': ['72', '73', '78']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '73', 'type': 'subscript', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'all_records'}; {'id': '75', 'type': 'slice', 'children': ['76', '77']}; {'id': '76', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '77', 'type': 'colon', 'children': []}; {'id': '78', 'type': 'block', 'children': ['79', '85', '89']}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'augmented_assignment', 'children': ['81', '82'], 'value': '+='}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'final_v'}; {'id': '82', 'type': 'subscript', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'items_by_key'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '85', 'type': 'delete_statement', 'children': ['86']}; {'id': '86', 'type': 'subscript', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'out_items_by_key'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '89', 'type': 'delete_statement', 'children': ['90']}; {'id': '90', 'type': 'subscript', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'out_input_order'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '98']}; {'id': '95', 'type': 'subscript', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'out_items_by_key'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'final_k'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'final_v'}; {'id': '99', 'type': 'return_statement', 'children': ['100']}; {'id': '100', 'type': 'expression_list', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'out_items_by_key'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'out_input_order'} | def _concat_records(items_by_key, input_order):
all_records = []
for (k, t) in input_order.items():
if t == "record":
all_records.append(k)
out_items_by_key = utils.deepish_copy(items_by_key)
out_input_order = utils.deepish_copy(input_order)
if len(all_records) > 1:
final_k = all_records[0]
final_v = items_by_key[final_k]
for k in all_records[1:]:
final_v += items_by_key[k]
del out_items_by_key[k]
del out_input_order[k]
out_items_by_key[final_k] = final_v
return out_items_by_key, out_input_order |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_combine_files'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'tsv_files'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'work_dir'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '7', 'type': 'block', 'children': ['8', '28', '37', '52', '122']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '11', 'type': 'call', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'string', 'children': [], 'value': '"\\t"'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'list', 'children': ['17', '18', '19', '20', '21', '22', '23', '24', '25', '26', '27'], 'value': '["caller", "sample", "chrom", "start", "end", "svtype",\n "lof", "annotation", "split_read_support", "paired_support_PE", "paired_support_PR"]'}; {'id': '17', 'type': 'string', 'children': [], 'value': '"caller"'}; {'id': '18', 'type': 'string', 'children': [], 'value': '"sample"'}; {'id': '19', 'type': 'string', 'children': [], 'value': '"chrom"'}; {'id': '20', 'type': 'string', 'children': [], 'value': '"start"'}; {'id': '21', 'type': 'string', 'children': [], 'value': '"end"'}; {'id': '22', 'type': 'string', 'children': [], 'value': '"svtype"'}; {'id': '23', 'type': 'string', 'children': [], 'value': '"lof"'}; {'id': '24', 'type': 'string', 'children': [], 'value': '"annotation"'}; {'id': '25', 'type': 'string', 'children': [], 'value': '"split_read_support"'}; {'id': '26', 'type': 'string', 'children': [], 'value': '"paired_support_PE"'}; {'id': '27', 'type': 'string', 'children': [], 'value': '"paired_support_PR"'}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}; {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '31', 'type': 'call', 'children': ['32', '35']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'get_sample_name'}; {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '40', 'type': 'call', 'children': ['41', '46']}; {'id': '41', 'type': 'attribute', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '46', 'type': 'argument_list', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'work_dir'}; {'id': '48', 'type': 'binary_operator', 'children': ['49', '50'], 'value': '%'}; {'id': '49', 'type': 'string', 'children': [], 'value': '"%s-prioritize.tsv"'}; {'id': '50', 'type': '()', 'children': ['51']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '52', 'type': 'if_statement', 'children': ['53', '60']}; {'id': '53', 'type': 'not_operator', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '60', 'type': 'block', 'children': ['61']}; {'id': '61', 'type': 'with_statement', 'children': ['62', '72']}; {'id': '62', 'type': 'with_clause', 'children': ['63']}; {'id': '63', 'type': 'with_item', 'children': ['64']}; {'id': '64', 'type': 'as_pattern', 'children': ['65', '70']}; {'id': '65', 'type': 'call', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '67', 'type': 'argument_list', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '70', 'type': 'as_pattern_target', 'children': ['71']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '72', 'type': 'block', 'children': ['73', '84', '93', '102', '106']}; {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'tmpdir'}; {'id': '76', 'type': 'call', 'children': ['77', '82']}; {'id': '77', 'type': 'attribute', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'dirname'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}; {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'input_files'}; {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}; {'id': '89', 'type': 'string', 'children': [], 'value': '" "'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'tsv_files'}; {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'sort_cmd'}; {'id': '96', 'type': 'call', 'children': ['97', '100']}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'bedutils'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'get_sort_cmd'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'tmpdir'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '105', 'type': 'string', 'children': [], 'value': '"{{ echo \'{header}\'; cat {input_files} | {sort_cmd} -k3,3 -k4,4n; }} > {tx_out_file}"'}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}; {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'do'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '111', 'type': 'argument_list', 'children': ['112', '121']}; {'id': '112', 'type': 'call', 'children': ['113', '116']}; {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '116', 'type': 'argument_list', 'children': ['117']}; {'id': '117', 'type': 'dictionary_splat', 'children': ['118']}; {'id': '118', 'type': 'call', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '120', 'type': 'argument_list', 'children': []}; {'id': '121', 'type': 'string', 'children': [], 'value': '"Combine prioritized from multiple callers"'}; {'id': '122', 'type': 'return_statement', 'children': ['123']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'out_file'} | def _combine_files(tsv_files, work_dir, data):
header = "\t".join(["caller", "sample", "chrom", "start", "end", "svtype",
"lof", "annotation", "split_read_support", "paired_support_PE", "paired_support_PR"])
sample = dd.get_sample_name(data)
out_file = os.path.join(work_dir, "%s-prioritize.tsv" % (sample))
if not utils.file_exists(out_file):
with file_transaction(data, out_file) as tx_out_file:
tmpdir = os.path.dirname(tx_out_file)
input_files = " ".join(tsv_files)
sort_cmd = bedutils.get_sort_cmd(tmpdir)
cmd = "{{ echo '{header}'; cat {input_files} | {sort_cmd} -k3,3 -k4,4n; }} > {tx_out_file}"
do.run(cmd.format(**locals()), "Combine prioritized from multiple callers")
return out_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_filenames'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'filenames'}; {'id': '5', 'type': 'block', 'children': ['6', '21', '45']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'basenames'}; {'id': '9', 'type': 'list_comprehension', 'children': ['10', '18']}; {'id': '10', 'type': 'call', 'children': ['11', '16']}; {'id': '11', 'type': 'attribute', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '16', 'type': 'argument_list', 'children': ['17']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '18', 'type': 'for_in_clause', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'filenames'}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'indexes'}; {'id': '24', 'type': 'list_comprehension', 'children': ['25', '28']}; {'id': '25', 'type': 'subscript', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '27', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '28', 'type': 'for_in_clause', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '30', 'type': 'call', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '37']}; {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'basenames'}; {'id': '37', 'type': 'keyword_argument', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '39', 'type': 'lambda', 'children': ['40', '42']}; {'id': '40', 'type': 'lambda_parameters', 'children': ['41']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '42', 'type': 'subscript', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '44', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '45', 'type': 'return_statement', 'children': ['46']}; {'id': '46', 'type': 'list_comprehension', 'children': ['47', '50']}; {'id': '47', 'type': 'subscript', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'filenames'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '50', 'type': 'for_in_clause', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'indexes'} | def sort_filenames(filenames):
basenames = [os.path.basename(x) for x in filenames]
indexes = [i[0] for i in sorted(enumerate(basenames), key=lambda x:x[1])]
return [filenames[x] for x in indexes] |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_csv'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '5', 'type': 'block', 'children': ['6', '12', '73']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '9', 'type': 'binary_operator', 'children': ['10', '11'], 'value': '%'}; {'id': '10', 'type': 'string', 'children': [], 'value': '"%s.sort"'}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '12', 'type': 'if_statement', 'children': ['13', '34']}; {'id': '13', 'type': 'not_operator', 'children': ['14']}; {'id': '14', 'type': '()', 'children': ['15']}; {'id': '15', 'type': 'boolean_operator', 'children': ['16', '24'], 'value': 'and'}; {'id': '16', 'type': 'call', 'children': ['17', '22']}; {'id': '17', 'type': 'attribute', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '33'], 'value': '>'}; {'id': '25', 'type': 'call', 'children': ['26', '31']}; {'id': '26', 'type': 'attribute', 'children': ['27', '30']}; {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'getsize'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '33', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '34', 'type': 'block', 'children': ['35', '43']}; {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'cl'}; {'id': '38', 'type': 'list', 'children': ['39', '40', '41', '42'], 'value': '["sort", "-k", "1,1", in_file]'}; {'id': '39', 'type': 'string', 'children': [], 'value': '"sort"'}; {'id': '40', 'type': 'string', 'children': [], 'value': '"-k"'}; {'id': '41', 'type': 'string', 'children': [], 'value': '"1,1"'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '43', 'type': 'with_statement', 'children': ['44', '54']}; {'id': '44', 'type': 'with_clause', 'children': ['45']}; {'id': '45', 'type': 'with_item', 'children': ['46']}; {'id': '46', 'type': 'as_pattern', 'children': ['47', '52']}; {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '49', 'type': 'argument_list', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '51', 'type': 'string', 'children': [], 'value': '"w"'}; {'id': '52', 'type': 'as_pattern_target', 'children': ['53']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '54', 'type': 'block', 'children': ['55', '67']}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '58', 'type': 'call', 'children': ['59', '62']}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'subprocess'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'Popen'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'cl'}; {'id': '64', 'type': 'keyword_argument', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'stdout'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'call', 'children': ['69', '72']}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'wait'}; {'id': '72', 'type': 'argument_list', 'children': []}; {'id': '73', 'type': 'return_statement', 'children': ['74']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'out_file'} | def sort_csv(in_file):
out_file = "%s.sort" % in_file
if not (os.path.exists(out_file) and os.path.getsize(out_file) > 0):
cl = ["sort", "-k", "1,1", in_file]
with open(out_file, "w") as out_handle:
child = subprocess.Popen(cl, stdout=out_handle)
child.wait()
return out_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'hydra_to_vcf_writer'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'hydra_file'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'genome_2bit'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '8', 'type': 'block', 'children': ['9', '14', '26', '39']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'call', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': '_write_vcf_header'}; {'id': '12', 'type': 'argument_list', 'children': ['13']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}; {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'brends'}; {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'call', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': '_get_vcf_breakends'}; {'id': '22', 'type': 'argument_list', 'children': ['23', '24', '25']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'hydra_file'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'genome_2bit'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'brends'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'keyword_argument', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '34', 'type': 'call', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'attrgetter'}; {'id': '36', 'type': 'argument_list', 'children': ['37', '38']}; {'id': '37', 'type': 'string', 'children': [], 'value': '"chrom"'}; {'id': '38', 'type': 'string', 'children': [], 'value': '"pos"'}; {'id': '39', 'type': 'for_statement', 'children': ['40', '41', '42']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'brend'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'brends'}; {'id': '42', 'type': 'block', 'children': ['43']}; {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'call', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': '_write_vcf_breakend'}; {'id': '46', 'type': 'argument_list', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'brend'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'out_handle'} | def hydra_to_vcf_writer(hydra_file, genome_2bit, options, out_handle):
_write_vcf_header(out_handle)
brends = list(_get_vcf_breakends(hydra_file, genome_2bit, options))
brends.sort(key=attrgetter("chrom", "pos"))
for brend in brends:
_write_vcf_breakend(brend, out_handle) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_split_by_ready_regions'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'ext'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'file_key'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'dir_ext_fn'}; {'id': '7', 'type': 'block', 'children': ['8', '30', '103', '251']}; {'id': '8', 'type': 'function_definition', 'children': ['9', '10', '12']}; {'id': '9', 'type': 'function_name', 'children': [], 'value': '_sort_by_size'}; {'id': '10', 'type': 'parameters', 'children': ['11']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'region_w_bams'}; {'id': '12', 'type': 'block', 'children': ['13', '19', '26']}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '18']}; {'id': '15', 'type': 'pattern_list', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'region_w_bams'}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '25']}; {'id': '21', 'type': 'pattern_list', 'children': ['22', '23', '24']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '26', 'type': 'return_statement', 'children': ['27']}; {'id': '27', 'type': 'binary_operator', 'children': ['28', '29'], 'value': '-'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '30', 'type': 'function_definition', 'children': ['31', '32', '34']}; {'id': '31', 'type': 'function_name', 'children': [], 'value': '_assign_bams_to_regions'}; {'id': '32', 'type': 'parameters', 'children': ['33']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '34', 'type': 'block', 'children': ['35']}; {'id': '35', 'type': 'for_statement', 'children': ['36', '39', '45']}; {'id': '36', 'type': 'pattern_list', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '39', 'type': 'call', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'subscript', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '44', 'type': 'string', 'children': [], 'value': '"region"'}; {'id': '45', 'type': 'block', 'children': ['46', '50', '84', '98']}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'work_bams'}; {'id': '49', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '50', 'type': 'for_statement', 'children': ['51', '52', '55']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'xs'}; {'id': '52', 'type': 'subscript', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '54', 'type': 'string', 'children': [], 'value': '"region_bams"'}; {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'if_statement', 'children': ['57', '63', '73']}; {'id': '57', 'type': 'comparison_operator', 'children': ['58', '62'], 'value': '=='}; {'id': '58', 'type': 'call', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'xs'}; {'id': '62', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '63', 'type': 'block', 'children': ['64']}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}; {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'work_bams'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'xs'}; {'id': '72', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '73', 'type': 'else_clause', 'children': ['74']}; {'id': '74', 'type': 'block', 'children': ['75']}; {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'call', 'children': ['77', '80']}; {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'work_bams'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '80', 'type': 'argument_list', 'children': ['81']}; {'id': '81', 'type': 'subscript', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'xs'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '84', 'type': 'for_statement', 'children': ['85', '86', '87']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'work_bam'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'work_bams'}; {'id': '87', 'type': 'block', 'children': ['88']}; {'id': '88', 'type': 'assert_statement', 'children': ['89', '97']}; {'id': '89', 'type': 'call', 'children': ['90', '95']}; {'id': '90', 'type': 'attribute', 'children': ['91', '94']}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'work_bam'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'work_bam'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}; {'id': '99', 'type': 'yield', 'children': ['100']}; {'id': '100', 'type': 'expression_list', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'work_bams'}; {'id': '103', 'type': 'function_definition', 'children': ['104', '105', '107']}; {'id': '104', 'type': 'function_name', 'children': [], 'value': '_do_work'}; {'id': '105', 'type': 'parameters', 'children': ['106']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '107', 'type': 'block', 'children': ['108']}; {'id': '108', 'type': 'if_statement', 'children': ['109', '112', '245']}; {'id': '109', 'type': 'comparison_operator', 'children': ['110', '111'], 'value': 'in'}; {'id': '110', 'type': 'string', 'children': [], 'value': '"region"'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '112', 'type': 'block', 'children': ['113', '128', '147', '163', '173', '177', '241']}; {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '116', 'type': 'conditional_expression', 'children': ['117', '122', '125'], 'value': 'if'}; {'id': '117', 'type': 'subscript', 'children': ['118', '121']}; {'id': '118', 'type': 'subscript', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '120', 'type': 'string', 'children': [], 'value': '"group"'}; {'id': '121', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '122', 'type': 'comparison_operator', 'children': ['123', '124'], 'value': 'in'}; {'id': '123', 'type': 'string', 'children': [], 'value': '"group"'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '125', 'type': 'subscript', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '127', 'type': 'string', 'children': [], 'value': '"description"'}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}; {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'out_dir'}; {'id': '131', 'type': 'call', 'children': ['132', '137']}; {'id': '132', 'type': 'attribute', 'children': ['133', '136']}; {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '137', 'type': 'argument_list', 'children': ['138', '143']}; {'id': '138', 'type': 'subscript', 'children': ['139', '142']}; {'id': '139', 'type': 'subscript', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '141', 'type': 'string', 'children': [], 'value': '"dirs"'}; {'id': '142', 'type': 'string', 'children': [], 'value': '"work"'}; {'id': '143', 'type': 'call', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'dir_ext_fn'}; {'id': '145', 'type': 'argument_list', 'children': ['146']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'assignment', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '150', 'type': 'call', 'children': ['151', '156']}; {'id': '151', 'type': 'attribute', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'out_dir'}; {'id': '158', 'type': 'binary_operator', 'children': ['159', '160'], 'value': '%'}; {'id': '159', 'type': 'string', 'children': [], 'value': '"%s%s"'}; {'id': '160', 'type': 'tuple', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'ext'}; {'id': '163', 'type': 'assert_statement', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '166', 'type': 'argument_list', 'children': ['167', '170']}; {'id': '167', 'type': 'subscript', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '169', 'type': 'string', 'children': [], 'value': '"region"'}; {'id': '170', 'type': 'tuple', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'assignment', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'out_parts'}; {'id': '176', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '177', 'type': 'for_statement', 'children': ['178', '181', '194']}; {'id': '178', 'type': 'pattern_list', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'work_bams'}; {'id': '181', 'type': 'call', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '183', 'type': 'argument_list', 'children': ['184', '188', '191']}; {'id': '184', 'type': 'call', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': '_assign_bams_to_regions'}; {'id': '186', 'type': 'argument_list', 'children': ['187']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '188', 'type': 'keyword_argument', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': '_sort_by_size'}; {'id': '191', 'type': 'keyword_argument', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '193', 'type': 'True', 'children': []}; {'id': '194', 'type': 'block', 'children': ['195', '209', '231']}; {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'out_region_dir'}; {'id': '198', 'type': 'call', 'children': ['199', '204']}; {'id': '199', 'type': 'attribute', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'out_dir'}; {'id': '206', 'type': 'subscript', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '208', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'assignment', 'children': ['211', '212']}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'out_region_file'}; {'id': '212', 'type': 'call', 'children': ['213', '218']}; {'id': '213', 'type': 'attribute', 'children': ['214', '217']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '218', 'type': 'argument_list', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'out_region_dir'}; {'id': '220', 'type': 'binary_operator', 'children': ['221', '222'], 'value': '%'}; {'id': '221', 'type': 'string', 'children': [], 'value': '"%s-%s%s"'}; {'id': '222', 'type': 'tuple', 'children': ['223', '224', '230']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '224', 'type': 'call', 'children': ['225', '228']}; {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'pregion'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'to_safestr'}; {'id': '228', 'type': 'argument_list', 'children': ['229']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'ext'}; {'id': '231', 'type': 'expression_statement', 'children': ['232']}; {'id': '232', 'type': 'call', 'children': ['233', '236']}; {'id': '233', 'type': 'attribute', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'out_parts'}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '236', 'type': 'argument_list', 'children': ['237']}; {'id': '237', 'type': 'tuple', 'children': ['238', '239', '240']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'work_bams'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'out_region_file'}; {'id': '241', 'type': 'return_statement', 'children': ['242']}; {'id': '242', 'type': 'expression_list', 'children': ['243', '244']}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'out_parts'}; {'id': '245', 'type': 'else_clause', 'children': ['246']}; {'id': '246', 'type': 'block', 'children': ['247']}; {'id': '247', 'type': 'return_statement', 'children': ['248']}; {'id': '248', 'type': 'expression_list', 'children': ['249', '250']}; {'id': '249', 'type': 'None', 'children': []}; {'id': '250', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '251', 'type': 'return_statement', 'children': ['252']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': '_do_work'} | def _split_by_ready_regions(ext, file_key, dir_ext_fn):
def _sort_by_size(region_w_bams):
region, _ = region_w_bams
_, start, end = region
return end - start
def _assign_bams_to_regions(data):
for i, region in enumerate(data["region"]):
work_bams = []
for xs in data["region_bams"]:
if len(xs) == 1:
work_bams.append(xs[0])
else:
work_bams.append(xs[i])
for work_bam in work_bams:
assert os.path.exists(work_bam), work_bam
yield region, work_bams
def _do_work(data):
if "region" in data:
name = data["group"][0] if "group" in data else data["description"]
out_dir = os.path.join(data["dirs"]["work"], dir_ext_fn(data))
out_file = os.path.join(out_dir, "%s%s" % (name, ext))
assert isinstance(data["region"], (list, tuple))
out_parts = []
for r, work_bams in sorted(_assign_bams_to_regions(data), key=_sort_by_size, reverse=True):
out_region_dir = os.path.join(out_dir, r[0])
out_region_file = os.path.join(out_region_dir,
"%s-%s%s" % (name, pregion.to_safestr(r), ext))
out_parts.append((r, work_bams, out_region_file))
return out_file, out_parts
else:
return None, []
return _do_work |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'ERROR', 'children': ['2', '137']}; {'id': '2', 'type': 'function_definition', 'children': ['3', '4', '9']}; {'id': '3', 'type': 'function_name', 'children': [], 'value': '_combine_variants'}; {'id': '4', 'type': 'parameters', 'children': ['5', '6', '7', '8']}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'in_vcfs'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '9', 'type': 'block', 'children': ['10', '16', '20', '121']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}; {'id': '11', 'type': 'call', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'in_vcfs'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '15', 'type': 'argument_list', 'children': []}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'wrote_header'}; {'id': '19', 'type': 'False', 'children': []}; {'id': '20', 'type': 'with_statement', 'children': ['21', '31']}; {'id': '21', 'type': 'with_clause', 'children': ['22']}; {'id': '22', 'type': 'with_item', 'children': ['23']}; {'id': '23', 'type': 'as_pattern', 'children': ['24', '29']}; {'id': '24', 'type': 'call', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '26', 'type': 'argument_list', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '28', 'type': 'string', 'children': [], 'value': '"w"'}; {'id': '29', 'type': 'as_pattern_target', 'children': ['30']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '31', 'type': 'block', 'children': ['32']}; {'id': '32', 'type': 'for_statement', 'children': ['33', '34', '42']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'in_vcf'}; {'id': '34', 'type': 'generator_expression', 'children': ['35', '39']}; {'id': '35', 'type': 'subscript', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '37', 'type': 'unary_operator', 'children': ['38'], 'value': '-'}; {'id': '38', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '39', 'type': 'for_in_clause', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'in_vcfs'}; {'id': '42', 'type': 'block', 'children': ['43']}; {'id': '43', 'type': 'with_statement', 'children': ['44', '53', '93']}; {'id': '44', 'type': 'with_clause', 'children': ['45']}; {'id': '45', 'type': 'with_item', 'children': ['46']}; {'id': '46', 'type': 'as_pattern', 'children': ['47', '51']}; {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'in_vcf'}; {'id': '51', 'type': 'as_pattern_target', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'in_handle'}; {'id': '53', 'type': 'ERROR', 'children': ['54', '55', '56', '71']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '56', 'type': 'call', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'itertools'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'takewhile'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'lambda', 'children': ['62', '64']}; {'id': '62', 'type': 'lambda_parameters', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '64', 'type': 'call', 'children': ['65', '68']}; {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '68', 'type': 'argument_list', 'children': ['69', '70']}; {'id': '69', 'type': 'ERROR', 'children': []}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'in_handle'}; {'id': '71', 'type': 'not_operator', 'children': ['72']}; {'id': '72', 'type': 'comparison_operator', 'children': ['73', '89', '92'], 'value': 'in'}; {'id': '73', 'type': 'call', 'children': ['74', '79']}; {'id': '74', 'type': 'attribute', 'children': ['75', '78']}; {'id': '75', 'type': 'subscript', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '77', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'binary_operator', 'children': ['81', '82', '86', '88'], 'value': '%'}; {'id': '81', 'type': 'string', 'children': [], 'value': '"\n raise ValueError("'}; {'id': '82', 'type': 'ERROR', 'children': ['83', '84', '85']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'Unexpected'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'VCF'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'file'}; {'id': '86', 'type': 'ERROR', 'children': ['87']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'in_vcf'}; {'id': '89', 'type': 'ERROR', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'for'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'in_handle'}; {'id': '93', 'type': 'block', 'children': ['94', '114']}; {'id': '94', 'type': 'if_statement', 'children': ['95', '97']}; {'id': '95', 'type': 'not_operator', 'children': ['96']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'wrote_header'}; {'id': '97', 'type': 'block', 'children': ['98', '102']}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}; {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'wrote_header'}; {'id': '101', 'type': 'True', 'children': []}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'call', 'children': ['109', '112']}; {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'string', 'children': [], 'value': '""'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}; {'id': '115', 'type': 'call', 'children': ['116', '119']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '119', 'type': 'argument_list', 'children': ['120']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '121', 'type': 'if_statement', 'children': ['122', '124']}; {'id': '122', 'type': 'not_operator', 'children': ['123']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'wrote_header'}; {'id': '124', 'type': 'block', 'children': ['125']}; {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'call', 'children': ['127', '130']}; {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}; {'id': '131', 'type': 'call', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}; {'id': '133', 'type': 'string', 'children': [], 'value': '""'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '135', 'type': 'argument_list', 'children': ['136']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '137', 'type': 'return_statement', 'children': ['138']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'out_file'} | def _combine_variants(in_vcfs, out_file, ref_file, config):
in_vcfs.sort()
wrote_header = False
with open(out_file, "w") as out_handle:
for in_vcf in (x[-1] for x in in_vcfs):
with open(in_vcf) as in_handle:
header = list(itertools.takewhile(lambda x: x.startswith("
in_handle))
if not header[0].startswith("
raise ValueError("Unexpected VCF file: %s" % in_vcf)
for line in in_handle:
if not wrote_header:
wrote_header = True
out_handle.write("".join(header))
out_handle.write(line)
if not wrote_header:
out_handle.write("".join(header))
return out_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'picard_sort'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'picard'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'sort_order'}; {'id': '8', 'type': 'string', 'children': [], 'value': '"coordinate"'}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'compression_level'}; {'id': '14', 'type': 'None', 'children': []}; {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'pipe'}; {'id': '17', 'type': 'False', 'children': []}; {'id': '18', 'type': 'block', 'children': ['19', '32', '45', '121']}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '24']}; {'id': '21', 'type': 'pattern_list', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'base'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'ext'}; {'id': '24', 'type': 'call', 'children': ['25', '30']}; {'id': '25', 'type': 'attribute', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'splitext'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '32', 'type': 'if_statement', 'children': ['33', '36']}; {'id': '33', 'type': 'comparison_operator', 'children': ['34', '35'], 'value': 'is'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '35', 'type': 'None', 'children': []}; {'id': '36', 'type': 'block', 'children': ['37']}; {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '40', 'type': 'binary_operator', 'children': ['41', '42'], 'value': '%'}; {'id': '41', 'type': 'string', 'children': [], 'value': '"%s-sort%s"'}; {'id': '42', 'type': 'tuple', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'base'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'ext'}; {'id': '45', 'type': 'if_statement', 'children': ['46', '51']}; {'id': '46', 'type': 'not_operator', 'children': ['47']}; {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'with_statement', 'children': ['53', '64']}; {'id': '53', 'type': 'with_clause', 'children': ['54']}; {'id': '54', 'type': 'with_item', 'children': ['55']}; {'id': '55', 'type': 'as_pattern', 'children': ['56', '62']}; {'id': '56', 'type': 'call', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'tx_tmpdir'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'picard'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': '_config'}; {'id': '62', 'type': 'as_pattern_target', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '64', 'type': 'block', 'children': ['65']}; {'id': '65', 'type': 'with_statement', 'children': ['66', '78']}; {'id': '66', 'type': 'with_clause', 'children': ['67']}; {'id': '67', 'type': 'with_item', 'children': ['68']}; {'id': '68', 'type': 'as_pattern', 'children': ['69', '76']}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '71', 'type': 'argument_list', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'picard'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': '_config'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '76', 'type': 'as_pattern_target', 'children': ['77']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '78', 'type': 'block', 'children': ['79', '98', '110']}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'opts'}; {'id': '82', 'type': 'list', 'children': ['83', '86', '92', '95'], 'value': '[("INPUT", align_bam),\n ("OUTPUT", out_file if pipe else tx_out_file),\n ("TMP_DIR", tmp_dir),\n ("SORT_ORDER", sort_order)]'}; {'id': '83', 'type': 'tuple', 'children': ['84', '85']}; {'id': '84', 'type': 'string', 'children': [], 'value': '"INPUT"'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'align_bam'}; {'id': '86', 'type': 'tuple', 'children': ['87', '88']}; {'id': '87', 'type': 'string', 'children': [], 'value': '"OUTPUT"'}; {'id': '88', 'type': 'conditional_expression', 'children': ['89', '90', '91'], 'value': 'if'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'pipe'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '92', 'type': 'tuple', 'children': ['93', '94']}; {'id': '93', 'type': 'string', 'children': [], 'value': '"TMP_DIR"'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '95', 'type': 'tuple', 'children': ['96', '97']}; {'id': '96', 'type': 'string', 'children': [], 'value': '"SORT_ORDER"'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'sort_order'}; {'id': '98', 'type': 'if_statement', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'compression_level'}; {'id': '100', 'type': 'block', 'children': ['101']}; {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'call', 'children': ['103', '106']}; {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'opts'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '106', 'type': 'argument_list', 'children': ['107']}; {'id': '107', 'type': 'tuple', 'children': ['108', '109']}; {'id': '108', 'type': 'string', 'children': [], 'value': '"COMPRESSION_LEVEL"'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'compression_level'}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}; {'id': '111', 'type': 'call', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'picard'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '115', 'type': 'argument_list', 'children': ['116', '117', '118']}; {'id': '116', 'type': 'string', 'children': [], 'value': '"SortSam"'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'opts'}; {'id': '118', 'type': 'keyword_argument', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'pipe'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'pipe'}; {'id': '121', 'type': 'return_statement', 'children': ['122']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'out_file'} | def picard_sort(picard, align_bam, sort_order="coordinate",
out_file=None, compression_level=None, pipe=False):
base, ext = os.path.splitext(align_bam)
if out_file is None:
out_file = "%s-sort%s" % (base, ext)
if not file_exists(out_file):
with tx_tmpdir(picard._config) as tmp_dir:
with file_transaction(picard._config, out_file) as tx_out_file:
opts = [("INPUT", align_bam),
("OUTPUT", out_file if pipe else tx_out_file),
("TMP_DIR", tmp_dir),
("SORT_ORDER", sort_order)]
if compression_level:
opts.append(("COMPRESSION_LEVEL", compression_level))
picard.run("SortSam", opts, pipe=pipe)
return out_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'picard_fix_rgs'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'picard'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '7', 'type': 'block', 'children': ['8', '23', '110']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '11', 'type': 'binary_operator', 'children': ['12', '13'], 'value': '%'}; {'id': '12', 'type': 'string', 'children': [], 'value': '"%s-fixrgs.bam"'}; {'id': '13', 'type': 'subscript', 'children': ['14', '22']}; {'id': '14', 'type': 'call', 'children': ['15', '20']}; {'id': '15', 'type': 'attribute', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'splitext'}; {'id': '20', 'type': 'argument_list', 'children': ['21']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '22', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '23', 'type': 'if_statement', 'children': ['24', '29']}; {'id': '24', 'type': 'not_operator', 'children': ['25']}; {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'with_statement', 'children': ['31', '42']}; {'id': '31', 'type': 'with_clause', 'children': ['32']}; {'id': '32', 'type': 'with_item', 'children': ['33']}; {'id': '33', 'type': 'as_pattern', 'children': ['34', '40']}; {'id': '34', 'type': 'call', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'tx_tmpdir'}; {'id': '36', 'type': 'argument_list', 'children': ['37']}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'picard'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': '_config'}; {'id': '40', 'type': 'as_pattern_target', 'children': ['41']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '42', 'type': 'block', 'children': ['43']}; {'id': '43', 'type': 'with_statement', 'children': ['44', '56']}; {'id': '44', 'type': 'with_clause', 'children': ['45']}; {'id': '45', 'type': 'with_item', 'children': ['46']}; {'id': '46', 'type': 'as_pattern', 'children': ['47', '54']}; {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '49', 'type': 'argument_list', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'picard'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': '_config'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '54', 'type': 'as_pattern_target', 'children': ['55']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '56', 'type': 'block', 'children': ['57', '102']}; {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'opts'}; {'id': '60', 'type': 'list', 'children': ['61', '64', '67', '70', '75', '84', '89', '94', '99'], 'value': '[("INPUT", in_bam),\n ("OUTPUT", tx_out_file),\n ("SORT_ORDER", "coordinate"),\n ("RGID", names["rg"]),\n ("RGLB", names.get("lb", "unknown")),\n ("RGPL", names["pl"]),\n ("RGPU", names["pu"]),\n ("RGSM", names["sample"]),\n ("TMP_DIR", tmp_dir)]'}; {'id': '61', 'type': 'tuple', 'children': ['62', '63']}; {'id': '62', 'type': 'string', 'children': [], 'value': '"INPUT"'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '64', 'type': 'tuple', 'children': ['65', '66']}; {'id': '65', 'type': 'string', 'children': [], 'value': '"OUTPUT"'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '67', 'type': 'tuple', 'children': ['68', '69']}; {'id': '68', 'type': 'string', 'children': [], 'value': '"SORT_ORDER"'}; {'id': '69', 'type': 'string', 'children': [], 'value': '"coordinate"'}; {'id': '70', 'type': 'tuple', 'children': ['71', '72']}; {'id': '71', 'type': 'string', 'children': [], 'value': '"RGID"'}; {'id': '72', 'type': 'subscript', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '74', 'type': 'string', 'children': [], 'value': '"rg"'}; {'id': '75', 'type': 'tuple', 'children': ['76', '77']}; {'id': '76', 'type': 'string', 'children': [], 'value': '"RGLB"'}; {'id': '77', 'type': 'call', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '81', 'type': 'argument_list', 'children': ['82', '83']}; {'id': '82', 'type': 'string', 'children': [], 'value': '"lb"'}; {'id': '83', 'type': 'string', 'children': [], 'value': '"unknown"'}; {'id': '84', 'type': 'tuple', 'children': ['85', '86']}; {'id': '85', 'type': 'string', 'children': [], 'value': '"RGPL"'}; {'id': '86', 'type': 'subscript', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '88', 'type': 'string', 'children': [], 'value': '"pl"'}; {'id': '89', 'type': 'tuple', 'children': ['90', '91']}; {'id': '90', 'type': 'string', 'children': [], 'value': '"RGPU"'}; {'id': '91', 'type': 'subscript', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '93', 'type': 'string', 'children': [], 'value': '"pu"'}; {'id': '94', 'type': 'tuple', 'children': ['95', '96']}; {'id': '95', 'type': 'string', 'children': [], 'value': '"RGSM"'}; {'id': '96', 'type': 'subscript', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '98', 'type': 'string', 'children': [], 'value': '"sample"'}; {'id': '99', 'type': 'tuple', 'children': ['100', '101']}; {'id': '100', 'type': 'string', 'children': [], 'value': '"TMP_DIR"'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'picard'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '107', 'type': 'argument_list', 'children': ['108', '109']}; {'id': '108', 'type': 'string', 'children': [], 'value': '"AddOrReplaceReadGroups"'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'opts'}; {'id': '110', 'type': 'return_statement', 'children': ['111']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'out_file'} | def picard_fix_rgs(picard, in_bam, names):
out_file = "%s-fixrgs.bam" % os.path.splitext(in_bam)[0]
if not file_exists(out_file):
with tx_tmpdir(picard._config) as tmp_dir:
with file_transaction(picard._config, out_file) as tx_out_file:
opts = [("INPUT", in_bam),
("OUTPUT", tx_out_file),
("SORT_ORDER", "coordinate"),
("RGID", names["rg"]),
("RGLB", names.get("lb", "unknown")),
("RGPL", names["pl"]),
("RGPU", names["pu"]),
("RGSM", names["sample"]),
("TMP_DIR", tmp_dir)]
picard.run("AddOrReplaceReadGroups", opts)
return out_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_enforce_max_region_size'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '15', '41', '52', '120']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'max_size'}; {'id': '10', 'type': 'integer', 'children': [], 'value': '20000'}; {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'overlap_size'}; {'id': '14', 'type': 'integer', 'children': [], 'value': '250'}; {'id': '15', 'type': 'function_definition', 'children': ['16', '17', '19']}; {'id': '16', 'type': 'function_name', 'children': [], 'value': '_has_larger_regions'}; {'id': '17', 'type': 'parameters', 'children': ['18']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '19', 'type': 'block', 'children': ['20']}; {'id': '20', 'type': 'return_statement', 'children': ['21']}; {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'any'}; {'id': '23', 'type': 'generator_expression', 'children': ['24', '33']}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '32'], 'value': '>'}; {'id': '25', 'type': 'binary_operator', 'children': ['26', '29'], 'value': '-'}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'max_size'}; {'id': '33', 'type': 'for_in_clause', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'pybedtools'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'BedTool'}; {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '44', 'type': 'binary_operator', 'children': ['45', '46'], 'value': '%'}; {'id': '45', 'type': 'string', 'children': [], 'value': '"%s-regionlimit%s"'}; {'id': '46', 'type': 'call', 'children': ['47', '50']}; {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '52', 'type': 'if_statement', 'children': ['53', '60']}; {'id': '53', 'type': 'not_operator', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '60', 'type': 'block', 'children': ['61']}; {'id': '61', 'type': 'if_statement', 'children': ['62', '66', '110']}; {'id': '62', 'type': 'call', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': '_has_larger_regions'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '66', 'type': 'block', 'children': ['67']}; {'id': '67', 'type': 'with_statement', 'children': ['68', '78']}; {'id': '68', 'type': 'with_clause', 'children': ['69']}; {'id': '69', 'type': 'with_item', 'children': ['70']}; {'id': '70', 'type': 'as_pattern', 'children': ['71', '76']}; {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '73', 'type': 'argument_list', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '76', 'type': 'as_pattern_target', 'children': ['77']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '78', 'type': 'block', 'children': ['79']}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '108']}; {'id': '81', 'type': 'attribute', 'children': ['82', '107']}; {'id': '82', 'type': 'call', 'children': ['83', '90']}; {'id': '83', 'type': 'attribute', 'children': ['84', '89']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}; {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'pybedtools'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'BedTool'}; {'id': '88', 'type': 'argument_list', 'children': []}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'window_maker'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '94', '99']}; {'id': '91', 'type': 'keyword_argument', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'w'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'max_size'}; {'id': '94', 'type': 'keyword_argument', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '96', 'type': 'binary_operator', 'children': ['97', '98'], 'value': '-'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'max_size'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'overlap_size'}; {'id': '99', 'type': 'keyword_argument', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'pybedtools'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'BedTool'}; {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'saveas'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '110', 'type': 'else_clause', 'children': ['111']}; {'id': '111', 'type': 'block', 'children': ['112']}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}; {'id': '113', 'type': 'call', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'symlink_plus'}; {'id': '117', 'type': 'argument_list', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '120', 'type': 'return_statement', 'children': ['121']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'out_file'} | def _enforce_max_region_size(in_file, data):
max_size = 20000
overlap_size = 250
def _has_larger_regions(f):
return any(r.stop - r.start > max_size for r in pybedtools.BedTool(f))
out_file = "%s-regionlimit%s" % utils.splitext_plus(in_file)
if not utils.file_exists(out_file):
if _has_larger_regions(in_file):
with file_transaction(data, out_file) as tx_out_file:
pybedtools.BedTool().window_maker(w=max_size,
s=max_size - overlap_size,
b=pybedtools.BedTool(in_file)).saveas(tx_out_file)
else:
utils.symlink_plus(in_file, out_file)
return out_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_prep_vrn_file'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'vcaller'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'work_dir'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'somatic_info'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'ignore_file'}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '10', 'type': 'block', 'children': ['11', '41', '71', '289']}; {'id': '11', 'type': 'if_statement', 'children': ['12', '18', '23', '32']}; {'id': '12', 'type': 'call', 'children': ['13', '16']}; {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'vcaller'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '16', 'type': 'argument_list', 'children': ['17']}; {'id': '17', 'type': 'string', 'children': [], 'value': '"vardict"'}; {'id': '18', 'type': 'block', 'children': ['19']}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'variant_type'}; {'id': '22', 'type': 'string', 'children': [], 'value': '"vardict"'}; {'id': '23', 'type': 'elif_clause', 'children': ['24', '27']}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '26'], 'value': '=='}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'vcaller'}; {'id': '26', 'type': 'string', 'children': [], 'value': '"mutect"'}; {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}; {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'variant_type'}; {'id': '31', 'type': 'string', 'children': [], 'value': '"mutect-smchet"'}; {'id': '32', 'type': 'else_clause', 'children': ['33']}; {'id': '33', 'type': 'block', 'children': ['34']}; {'id': '34', 'type': 'raise_statement', 'children': ['35']}; {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'binary_operator', 'children': ['39', '40'], 'value': '%'}; {'id': '39', 'type': 'string', 'children': [], 'value': '"Unexpected variant caller for PhyloWGS prep: %s"'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'vcaller'}; {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '44', 'type': 'call', 'children': ['45', '50']}; {'id': '45', 'type': 'attribute', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '50', 'type': 'argument_list', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'work_dir'}; {'id': '52', 'type': 'binary_operator', 'children': ['53', '54'], 'value': '%'}; {'id': '53', 'type': 'string', 'children': [], 'value': '"%s-%s-prep.vcf"'}; {'id': '54', 'type': 'tuple', 'children': ['55', '70']}; {'id': '55', 'type': 'subscript', 'children': ['56', '69']}; {'id': '56', 'type': 'call', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'call', 'children': ['62', '67']}; {'id': '62', 'type': 'attribute', 'children': ['63', '66']}; {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '69', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'vcaller'}; {'id': '71', 'type': 'if_statement', 'children': ['72', '80']}; {'id': '72', 'type': 'not_operator', 'children': ['73']}; {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'file_uptodate'}; {'id': '77', 'type': 'argument_list', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '80', 'type': 'block', 'children': ['81', '88']}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'check_fn'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': '_min_sample_pass'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'ignore_file'}; {'id': '88', 'type': 'with_statement', 'children': ['89', '101']}; {'id': '89', 'type': 'with_clause', 'children': ['90']}; {'id': '90', 'type': 'with_item', 'children': ['91']}; {'id': '91', 'type': 'as_pattern', 'children': ['92', '99']}; {'id': '92', 'type': 'call', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '98']}; {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'somatic_info'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'tumor_data'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '99', 'type': 'as_pattern_target', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '101', 'type': 'block', 'children': ['102', '113', '167', '228']}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'tx_out_file_raw'}; {'id': '105', 'type': 'binary_operator', 'children': ['106', '107'], 'value': '%'}; {'id': '106', 'type': 'string', 'children': [], 'value': '"%s-raw%s"'}; {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '113', 'type': 'with_statement', 'children': ['114', '123']}; {'id': '114', 'type': 'with_clause', 'children': ['115']}; {'id': '115', 'type': 'with_item', 'children': ['116']}; {'id': '116', 'type': 'as_pattern', 'children': ['117', '121']}; {'id': '117', 'type': 'call', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'VariantFile'}; {'id': '119', 'type': 'argument_list', 'children': ['120']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '121', 'type': 'as_pattern_target', 'children': ['122']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'bcf_in'}; {'id': '123', 'type': 'block', 'children': ['124', '142', '151']}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}; {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'depths'}; {'id': '127', 'type': 'list_comprehension', 'children': ['128', '135']}; {'id': '128', 'type': 'call', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': '_sample_depth'}; {'id': '130', 'type': 'argument_list', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'somatic_info'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'tumor_name'}; {'id': '135', 'type': 'for_in_clause', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '137', 'type': 'call', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '139', 'type': 'argument_list', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'check_fn'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'bcf_in'}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}; {'id': '143', 'type': 'call', 'children': ['144', '147']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'depths'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'keyword_argument', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '150', 'type': 'True', 'children': []}; {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'assignment', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'depth_thresh'}; {'id': '154', 'type': 'conditional_expression', 'children': ['155', '165', '166'], 'value': 'if'}; {'id': '155', 'type': 'subscript', 'children': ['156', '163']}; {'id': '156', 'type': 'subscript', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'depths'}; {'id': '158', 'type': 'slice', 'children': ['159', '160']}; {'id': '159', 'type': 'colon', 'children': []}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '162', 'type': 'string', 'children': [], 'value': '"sample_size"'}; {'id': '163', 'type': 'unary_operator', 'children': ['164'], 'value': '-'}; {'id': '164', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'depths'}; {'id': '166', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '167', 'type': 'with_statement', 'children': ['168', '177']}; {'id': '168', 'type': 'with_clause', 'children': ['169']}; {'id': '169', 'type': 'with_item', 'children': ['170']}; {'id': '170', 'type': 'as_pattern', 'children': ['171', '175']}; {'id': '171', 'type': 'call', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'VariantFile'}; {'id': '173', 'type': 'argument_list', 'children': ['174']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '175', 'type': 'as_pattern_target', 'children': ['176']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'bcf_in'}; {'id': '177', 'type': 'block', 'children': ['178']}; {'id': '178', 'type': 'with_statement', 'children': ['179', '194']}; {'id': '179', 'type': 'with_clause', 'children': ['180']}; {'id': '180', 'type': 'with_item', 'children': ['181']}; {'id': '181', 'type': 'as_pattern', 'children': ['182', '192']}; {'id': '182', 'type': 'call', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'VariantFile'}; {'id': '184', 'type': 'argument_list', 'children': ['185', '186', '187']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'tx_out_file_raw'}; {'id': '186', 'type': 'string', 'children': [], 'value': '"w"'}; {'id': '187', 'type': 'keyword_argument', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'bcf_in'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '192', 'type': 'as_pattern_target', 'children': ['193']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'bcf_out'}; {'id': '194', 'type': 'block', 'children': ['195']}; {'id': '195', 'type': 'for_statement', 'children': ['196', '197', '198']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'bcf_in'}; {'id': '198', 'type': 'block', 'children': ['199']}; {'id': '199', 'type': 'if_statement', 'children': ['200', '220']}; {'id': '200', 'type': '()', 'children': ['201']}; {'id': '201', 'type': 'boolean_operator', 'children': ['202', '206'], 'value': 'and'}; {'id': '202', 'type': 'call', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'check_fn'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '206', 'type': '()', 'children': ['207']}; {'id': '207', 'type': 'boolean_operator', 'children': ['208', '211'], 'value': 'or'}; {'id': '208', 'type': 'comparison_operator', 'children': ['209', '210'], 'value': '<'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'depth_thresh'}; {'id': '210', 'type': 'integer', 'children': [], 'value': '5'}; {'id': '211', 'type': 'comparison_operator', 'children': ['212', '219'], 'value': '>='}; {'id': '212', 'type': 'call', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': '_sample_depth'}; {'id': '214', 'type': 'argument_list', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'somatic_info'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'tumor_name'}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'depth_thresh'}; {'id': '220', 'type': 'block', 'children': ['221']}; {'id': '221', 'type': 'expression_statement', 'children': ['222']}; {'id': '222', 'type': 'call', 'children': ['223', '226']}; {'id': '223', 'type': 'attribute', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'bcf_out'}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '226', 'type': 'argument_list', 'children': ['227']}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '228', 'type': 'with_statement', 'children': ['229', '238']}; {'id': '229', 'type': 'with_clause', 'children': ['230']}; {'id': '230', 'type': 'with_item', 'children': ['231']}; {'id': '231', 'type': 'as_pattern', 'children': ['232', '236']}; {'id': '232', 'type': 'call', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '234', 'type': 'argument_list', 'children': ['235']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'tx_out_file_raw'}; {'id': '236', 'type': 'as_pattern_target', 'children': ['237']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'in_handle'}; {'id': '238', 'type': 'block', 'children': ['239']}; {'id': '239', 'type': 'with_statement', 'children': ['240', '250']}; {'id': '240', 'type': 'with_clause', 'children': ['241']}; {'id': '241', 'type': 'with_item', 'children': ['242']}; {'id': '242', 'type': 'as_pattern', 'children': ['243', '248']}; {'id': '243', 'type': 'call', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '245', 'type': 'argument_list', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '247', 'type': 'string', 'children': [], 'value': '"w"'}; {'id': '248', 'type': 'as_pattern_target', 'children': ['249']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '250', 'type': 'block', 'children': ['251']}; {'id': '251', 'type': 'for_statement', 'children': ['252', '253', '254', '288']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'in_handle'}; {'id': '254', 'type': 'ERROR', 'children': ['255', '282']}; {'id': '255', 'type': 'ERROR', 'children': ['256', '269', '275', '276']}; {'id': '256', 'type': 'not_operator', 'children': ['257']}; {'id': '257', 'type': 'subscript', 'children': ['258', '266', '268']}; {'id': '258', 'type': 'call', 'children': ['259', '262']}; {'id': '259', 'type': 'attribute', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '262', 'type': 'argument_list', 'children': ['263', '264']}; {'id': '263', 'type': 'string', 'children': [], 'value': '"\n parts = line.split("'}; {'id': '264', 'type': 'ERROR', 'children': ['265']}; {'id': '265', 'type': 'escape_sequence', 'children': [], 'value': '\\t'}; {'id': '266', 'type': 'ERROR', 'children': ['267']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'parts'}; {'id': '268', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '269', 'type': 'call', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': '_phylowgs_compatible_chroms'}; {'id': '271', 'type': 'argument_list', 'children': ['272']}; {'id': '272', 'type': 'subscript', 'children': ['273', '274']}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'parts'}; {'id': '274', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '276', 'type': 'call', 'children': ['277', '280']}; {'id': '277', 'type': 'attribute', 'children': ['278', '279']}; {'id': '278', 'type': 'string', 'children': [], 'value': '"\\t"'}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '280', 'type': 'argument_list', 'children': ['281']}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'parts'}; {'id': '282', 'type': 'call', 'children': ['283', '286']}; {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '286', 'type': 'argument_list', 'children': ['287']}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '288', 'type': 'block', 'children': [], 'value': ''}; {'id': '289', 'type': 'return_statement', 'children': ['290']}; {'id': '290', 'type': 'expression_list', 'children': ['291', '292']}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'variant_type'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'out_file'} | def _prep_vrn_file(in_file, vcaller, work_dir, somatic_info, ignore_file, config):
if vcaller.startswith("vardict"):
variant_type = "vardict"
elif vcaller == "mutect":
variant_type = "mutect-smchet"
else:
raise ValueError("Unexpected variant caller for PhyloWGS prep: %s" % vcaller)
out_file = os.path.join(work_dir, "%s-%s-prep.vcf" % (utils.splitext_plus(os.path.basename(in_file))[0],
vcaller))
if not utils.file_uptodate(out_file, in_file):
check_fn = _min_sample_pass(ignore_file)
with file_transaction(somatic_info.tumor_data, out_file) as tx_out_file:
tx_out_file_raw = "%s-raw%s" % utils.splitext_plus(tx_out_file)
with VariantFile(in_file) as bcf_in:
depths = [_sample_depth(rec, somatic_info.tumor_name) for rec in
filter(check_fn, bcf_in)]
depths.sort(reverse=True)
depth_thresh = depths[:config["sample_size"]][-1] if depths else 0
with VariantFile(in_file) as bcf_in:
with VariantFile(tx_out_file_raw, "w", header=bcf_in.header) as bcf_out:
for rec in bcf_in:
if (check_fn(rec) and
(depth_thresh < 5 or _sample_depth(rec, somatic_info.tumor_name) >= depth_thresh)):
bcf_out.write(rec)
with open(tx_out_file_raw) as in_handle:
with open(tx_out_file, "w") as out_handle:
for line in in_handle:
if not line.startswith("
parts = line.split("\t")
parts[0] = _phylowgs_compatible_chroms(parts[0])
line = "\t".join(parts)
out_handle.write(line)
return variant_type, out_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'concat'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'bed_files'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'catted'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '19', '68', '113']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'bed_files'}; {'id': '12', 'type': 'list_comprehension', 'children': ['13', '14', '17']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '14', 'type': 'for_in_clause', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'bed_files'}; {'id': '17', 'type': 'if_clause', 'children': ['18']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '19', 'type': 'if_statement', 'children': ['20', '26']}; {'id': '20', 'type': 'comparison_operator', 'children': ['21', '25'], 'value': '=='}; {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'bed_files'}; {'id': '25', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '26', 'type': 'block', 'children': ['27']}; {'id': '27', 'type': 'if_statement', 'children': ['28', '29', '64']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'catted'}; {'id': '29', 'type': 'block', 'children': ['30', '38']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'sorted_bed'}; {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'catted'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '37', 'type': 'argument_list', 'children': []}; {'id': '38', 'type': 'if_statement', 'children': ['39', '48', '60']}; {'id': '39', 'type': 'not_operator', 'children': ['40']}; {'id': '40', 'type': 'call', 'children': ['41', '46']}; {'id': '41', 'type': 'attribute', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'sorted_bed'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'fn'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}; {'id': '47', 'type': 'string', 'children': [], 'value': '".bed"'}; {'id': '48', 'type': 'block', 'children': ['49']}; {'id': '49', 'type': 'return_statement', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'sorted_bed'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'moveto'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}; {'id': '55', 'type': 'binary_operator', 'children': ['56', '59'], 'value': '+'}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'sorted_bed'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'fn'}; {'id': '59', 'type': 'string', 'children': [], 'value': '".bed"'}; {'id': '60', 'type': 'else_clause', 'children': ['61']}; {'id': '61', 'type': 'block', 'children': ['62']}; {'id': '62', 'type': 'return_statement', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'sorted_bed'}; {'id': '64', 'type': 'else_clause', 'children': ['65']}; {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'return_statement', 'children': ['67']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'catted'}; {'id': '68', 'type': 'if_statement', 'children': ['69', '71', '92']}; {'id': '69', 'type': 'not_operator', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'catted'}; {'id': '71', 'type': 'block', 'children': ['72', '79']}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}; {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'bed_files'}; {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'bed_files'}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'catted'}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'bt'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'BedTool'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'bed_files'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '91', 'type': 'argument_list', 'children': []}; {'id': '92', 'type': 'else_clause', 'children': ['93']}; {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'catted'}; {'id': '97', 'type': 'call', 'children': ['98', '101']}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'catted'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '101', 'type': 'argument_list', 'children': ['102', '107', '110']}; {'id': '102', 'type': 'call', 'children': ['103', '106']}; {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'bed_files'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '106', 'type': 'argument_list', 'children': []}; {'id': '107', 'type': 'keyword_argument', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'postmerge'}; {'id': '109', 'type': 'False', 'children': []}; {'id': '110', 'type': 'keyword_argument', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'force_truncate'}; {'id': '112', 'type': 'False', 'children': []}; {'id': '113', 'type': 'return_statement', 'children': ['114']}; {'id': '114', 'type': 'call', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'concat'}; {'id': '116', 'type': 'argument_list', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'bed_files'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'catted'} | def concat(bed_files, catted=None):
bed_files = [x for x in bed_files if x]
if len(bed_files) == 0:
if catted:
sorted_bed = catted.sort()
if not sorted_bed.fn.endswith(".bed"):
return sorted_bed.moveto(sorted_bed.fn + ".bed")
else:
return sorted_bed
else:
return catted
if not catted:
bed_files = list(bed_files)
catted = bt.BedTool(bed_files.pop())
else:
catted = catted.cat(bed_files.pop(), postmerge=False,
force_truncate=False)
return concat(bed_files, catted) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_sv_callers'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '5', 'type': 'block', 'children': ['6', '10', '33']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'callers'}; {'id': '9', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '10', 'type': 'for_statement', 'children': ['11', '12', '13']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'for_statement', 'children': ['15', '16', '23']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'sv'}; {'id': '16', 'type': 'call', 'children': ['17', '20']}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '20', 'type': 'argument_list', 'children': ['21', '22']}; {'id': '21', 'type': 'string', 'children': [], 'value': '"sv"'}; {'id': '22', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '23', 'type': 'block', 'children': ['24']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}; {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'callers'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '29', 'type': 'argument_list', 'children': ['30']}; {'id': '30', 'type': 'subscript', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'sv'}; {'id': '32', 'type': 'string', 'children': [], 'value': '"variantcaller"'}; {'id': '33', 'type': 'return_statement', 'children': ['34']}; {'id': '34', 'type': 'call', 'children': ['35', '52']}; {'id': '35', 'type': 'attribute', 'children': ['36', '51']}; {'id': '36', 'type': 'call', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}; {'id': '39', 'type': 'call', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'list_comprehension', 'children': ['43', '44', '47']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '44', 'type': 'for_in_clause', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'callers'}; {'id': '47', 'type': 'if_clause', 'children': ['48']}; {'id': '48', 'type': 'comparison_operator', 'children': ['49', '50'], 'value': '!='}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '50', 'type': 'string', 'children': [], 'value': '"sv-ensemble"'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '52', 'type': 'argument_list', 'children': []} | def _get_sv_callers(items):
callers = []
for data in items:
for sv in data.get("sv", []):
callers.append(sv["variantcaller"])
return list(set([x for x in callers if x != "sv-ensemble"])).sort() |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_sort_cmd'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'default_parameter', 'children': ['5', '6']}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '6', 'type': 'None', 'children': []}; {'id': '7', 'type': 'block', 'children': ['8', '24', '37', '64']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'has_versionsort'}; {'id': '11', 'type': 'call', 'children': ['12', '23']}; {'id': '12', 'type': 'attribute', 'children': ['13', '22']}; {'id': '13', 'type': 'call', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'subprocess'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'check_output'}; {'id': '17', 'type': 'argument_list', 'children': ['18', '19']}; {'id': '18', 'type': 'string', 'children': [], 'value': '"sort --help | grep version-sort; exit 0"'}; {'id': '19', 'type': 'keyword_argument', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'shell'}; {'id': '21', 'type': 'True', 'children': []}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'strip'}; {'id': '23', 'type': 'argument_list', 'children': []}; {'id': '24', 'type': 'if_statement', 'children': ['25', '26', '31']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'has_versionsort'}; {'id': '26', 'type': 'block', 'children': ['27']}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '30', 'type': 'string', 'children': [], 'value': '"sort -V"'}; {'id': '31', 'type': 'else_clause', 'children': ['32']}; {'id': '32', 'type': 'block', 'children': ['33']}; {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '36', 'type': 'string', 'children': [], 'value': '"sort"'}; {'id': '37', 'type': 'if_statement', 'children': ['38', '57']}; {'id': '38', 'type': 'boolean_operator', 'children': ['39', '49'], 'value': 'and'}; {'id': '39', 'type': 'boolean_operator', 'children': ['40', '41'], 'value': 'and'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '41', 'type': 'call', 'children': ['42', '47']}; {'id': '42', 'type': 'attribute', 'children': ['43', '46']}; {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '49', 'type': 'call', 'children': ['50', '55']}; {'id': '50', 'type': 'attribute', 'children': ['51', '54']}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'isdir'}; {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '57', 'type': 'block', 'children': ['58']}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}; {'id': '59', 'type': 'augmented_assignment', 'children': ['60', '61'], 'value': '+='}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '61', 'type': 'binary_operator', 'children': ['62', '63'], 'value': '%'}; {'id': '62', 'type': 'string', 'children': [], 'value': '" -T %s"'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '64', 'type': 'return_statement', 'children': ['65']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'cmd'} | def get_sort_cmd(tmp_dir=None):
has_versionsort = subprocess.check_output("sort --help | grep version-sort; exit 0", shell=True).strip()
if has_versionsort:
cmd = "sort -V"
else:
cmd = "sort"
if tmp_dir and os.path.exists(tmp_dir) and os.path.isdir(tmp_dir):
cmd += " -T %s" % tmp_dir
return cmd |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '15']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'clean_file'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '8', 'type': 'string', 'children': [], 'value': '""'}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'bedprep_dir'}; {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'simple'}; {'id': '14', 'type': 'None', 'children': []}; {'id': '15', 'type': 'block', 'children': ['16', '23']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'simple'}; {'id': '19', 'type': 'conditional_expression', 'children': ['20', '21', '22'], 'value': 'if'}; {'id': '20', 'type': 'string', 'children': [], 'value': '"iconv -c -f utf-8 -t ascii | sed \'s/ //g\' |"'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'simple'}; {'id': '22', 'type': 'string', 'children': [], 'value': '""'}; {'id': '23', 'type': 'if_statement', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '25', 'type': 'block', 'children': ['26', '51', '70', '93', '103', '120', '216', '233']}; {'id': '26', 'type': 'if_statement', 'children': ['27', '29']}; {'id': '27', 'type': 'not_operator', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'bedprep_dir'}; {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'bedprep_dir'}; {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'safe_makedir'}; {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'call', 'children': ['39', '44']}; {'id': '39', 'type': 'attribute', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '44', 'type': 'argument_list', 'children': ['45', '50']}; {'id': '45', 'type': 'subscript', 'children': ['46', '49']}; {'id': '46', 'type': 'subscript', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '48', 'type': 'string', 'children': [], 'value': '"dirs"'}; {'id': '49', 'type': 'string', 'children': [], 'value': '"work"'}; {'id': '50', 'type': 'string', 'children': [], 'value': '"bedprep"'}; {'id': '51', 'type': 'if_statement', 'children': ['52', '67']}; {'id': '52', 'type': 'boolean_operator', 'children': ['53', '54'], 'value': 'and'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '54', 'type': 'call', 'children': ['55', '65']}; {'id': '55', 'type': 'attribute', 'children': ['56', '64']}; {'id': '56', 'type': 'call', 'children': ['57', '62']}; {'id': '57', 'type': 'attribute', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '67', 'type': 'block', 'children': ['68']}; {'id': '68', 'type': 'return_statement', 'children': ['69']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}; {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '73', 'type': 'call', 'children': ['74', '79']}; {'id': '74', 'type': 'attribute', 'children': ['75', '78']}; {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '79', 'type': 'argument_list', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'bedprep_dir'}; {'id': '81', 'type': 'binary_operator', 'children': ['82', '83'], 'value': '%'}; {'id': '82', 'type': 'string', 'children': [], 'value': '"%s%s"'}; {'id': '83', 'type': 'tuple', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '85', 'type': 'call', 'children': ['86', '91']}; {'id': '86', 'type': 'attribute', 'children': ['87', '90']}; {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '96', 'type': 'call', 'children': ['97', '100']}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '100', 'type': 'argument_list', 'children': ['101', '102']}; {'id': '101', 'type': 'string', 'children': [], 'value': '".interval_list"'}; {'id': '102', 'type': 'string', 'children': [], 'value': '".bed"'}; {'id': '103', 'type': 'if_statement', 'children': ['104', '110']}; {'id': '104', 'type': 'call', 'children': ['105', '108']}; {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}; {'id': '109', 'type': 'string', 'children': [], 'value': '".gz"'}; {'id': '110', 'type': 'block', 'children': ['111']}; {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '116', 'type': 'slice', 'children': ['117', '118']}; {'id': '117', 'type': 'colon', 'children': []}; {'id': '118', 'type': 'unary_operator', 'children': ['119'], 'value': '-'}; {'id': '119', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '120', 'type': 'if_statement', 'children': ['121', '129']}; {'id': '121', 'type': 'not_operator', 'children': ['122']}; {'id': '122', 'type': 'call', 'children': ['123', '126']}; {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'file_uptodate'}; {'id': '126', 'type': 'argument_list', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '129', 'type': 'block', 'children': ['130', '136', '142']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}; {'id': '131', 'type': 'call', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'check_bed_contigs'}; {'id': '133', 'type': 'argument_list', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}; {'id': '137', 'type': 'call', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'check_bed_coords'}; {'id': '139', 'type': 'argument_list', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '142', 'type': 'with_statement', 'children': ['143', '153']}; {'id': '143', 'type': 'with_clause', 'children': ['144']}; {'id': '144', 'type': 'with_item', 'children': ['145']}; {'id': '145', 'type': 'as_pattern', 'children': ['146', '151']}; {'id': '146', 'type': 'call', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '148', 'type': 'argument_list', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '151', 'type': 'as_pattern_target', 'children': ['152']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '153', 'type': 'block', 'children': ['154', '160', '172', '186', '199']}; {'id': '154', 'type': 'expression_statement', 'children': ['155']}; {'id': '155', 'type': 'assignment', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'bcbio_py'}; {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'executable'}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}; {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'cat_cmd'}; {'id': '163', 'type': 'conditional_expression', 'children': ['164', '165', '171'], 'value': 'if'}; {'id': '164', 'type': 'string', 'children': [], 'value': '"zcat"'}; {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'in_file'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'string', 'children': [], 'value': '".gz"'}; {'id': '171', 'type': 'string', 'children': [], 'value': '"cat"'}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}; {'id': '173', 'type': 'assignment', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'sort_cmd'}; {'id': '175', 'type': 'call', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'get_sort_cmd'}; {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'call', 'children': ['179', '184']}; {'id': '179', 'type': 'attribute', 'children': ['180', '183']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'dirname'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}; {'id': '187', 'type': 'assignment', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '189', 'type': '()', 'children': ['190']}; {'id': '190', 'type': 'binary_operator', 'children': ['191', '196'], 'value': '^'}; {'id': '191', 'type': 'binary_operator', 'children': ['192', '193', '195'], 'value': '-'}; {'id': '192', 'type': 'string', 'children': [], 'value': '"{cat_cmd} {in_file} | grep -v ^track | grep -v ^browser | grep -v ^@ | "'}; {'id': '193', 'type': 'ERROR', 'children': ['194']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'grep'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '196', 'type': 'concatenated_string', 'children': ['197', '198']}; {'id': '197', 'type': 'string', 'children': [], 'value': '"{bcbio_py} -c \'from bcbio.variation import bedutils; bedutils.remove_bad()\' | "'}; {'id': '198', 'type': 'string', 'children': [], 'value': '"{sort_cmd} -k1,1 -k2,2n > {tx_out_file}"'}; {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'call', 'children': ['201', '204']}; {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'do'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '214', '215']}; {'id': '205', 'type': 'call', 'children': ['206', '209']}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'dictionary_splat', 'children': ['211']}; {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '213', 'type': 'argument_list', 'children': []}; {'id': '214', 'type': 'string', 'children': [], 'value': '"Prepare cleaned BED file"'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}; {'id': '217', 'type': 'call', 'children': ['218', '221']}; {'id': '218', 'type': 'attribute', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'vcfutils'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'bgzip_and_index'}; {'id': '221', 'type': 'argument_list', 'children': ['222', '223', '230']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '223', 'type': 'call', 'children': ['224', '227']}; {'id': '224', 'type': 'attribute', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '227', 'type': 'argument_list', 'children': ['228', '229']}; {'id': '228', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '229', 'type': 'dictionary', 'children': []}; {'id': '230', 'type': 'keyword_argument', 'children': ['231', '232']}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'remove_orig'}; {'id': '232', 'type': 'False', 'children': []}; {'id': '233', 'type': 'return_statement', 'children': ['234']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'out_file'} | def clean_file(in_file, data, prefix="", bedprep_dir=None, simple=None):
simple = "iconv -c -f utf-8 -t ascii | sed 's/ //g' |" if simple else ""
if in_file:
if not bedprep_dir:
bedprep_dir = utils.safe_makedir(os.path.join(data["dirs"]["work"], "bedprep"))
if prefix and os.path.basename(in_file).startswith(prefix):
return in_file
out_file = os.path.join(bedprep_dir, "%s%s" % (prefix, os.path.basename(in_file)))
out_file = out_file.replace(".interval_list", ".bed")
if out_file.endswith(".gz"):
out_file = out_file[:-3]
if not utils.file_uptodate(out_file, in_file):
check_bed_contigs(in_file, data)
check_bed_coords(in_file, data)
with file_transaction(data, out_file) as tx_out_file:
bcbio_py = sys.executable
cat_cmd = "zcat" if in_file.endswith(".gz") else "cat"
sort_cmd = get_sort_cmd(os.path.dirname(tx_out_file))
cmd = ("{cat_cmd} {in_file} | grep -v ^track | grep -v ^browser | grep -v ^@ | "
"grep -v ^
"{bcbio_py} -c 'from bcbio.variation import bedutils; bedutils.remove_bad()' | "
"{sort_cmd} -k1,1 -k2,2n > {tx_out_file}")
do.run(cmd.format(**locals()), "Prepare cleaned BED file", data)
vcfutils.bgzip_and_index(out_file, data.get("config", {}), remove_orig=False)
return out_file |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_sort_by_region'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'fnames'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'regions'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '8', 'type': 'block', 'children': ['9', '13', '36', '40', '53', '60', '174', '180']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'contig_order'}; {'id': '12', 'type': 'dictionary', 'children': []}; {'id': '13', 'type': 'for_statement', 'children': ['14', '17', '27']}; {'id': '14', 'type': 'pattern_list', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'sq'}; {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'call', 'children': ['21', '24']}; {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'file_contigs'}; {'id': '24', 'type': 'argument_list', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}; {'id': '29', 'type': 'assignment', 'children': ['30', '35']}; {'id': '30', 'type': 'subscript', 'children': ['31', '32']}; 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{'id': '46', 'type': 'call', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'fnames'}; {'id': '50', 'type': 'tuple', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'regions'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'fnames'}; {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'added_fnames'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '60', 'type': 'for_statement', 'children': ['61', '64', '69']}; {'id': '61', 'type': 'pattern_list', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'fname'}; {'id': '64', 'type': 'call', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '66', 'type': 'argument_list', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'regions'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'fnames'}; {'id': '69', 'type': 'block', 'children': ['70']}; {'id': '70', 'type': 'if_statement', 'children': ['71', '74']}; {'id': '71', 'type': 'comparison_operator', 'children': ['72', '73'], 'value': 'not'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'fname'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'added_fnames'}; {'id': '74', 'type': 'block', 'children': ['75', '152', '167']}; {'id': '75', 'type': 'if_statement', 'children': ['76', '83', '91', '138']}; {'id': '76', 'type': 'call', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '78', 'type': 'argument_list', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '80', 'type': 'tuple', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '83', 'type': 'block', 'children': ['84']}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}; {'id': '85', 'type': 'assignment', 'children': ['86', '90']}; {'id': '86', 'type': 'pattern_list', 'children': ['87', '88', '89']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '91', 'type': 'elif_clause', 'children': ['92', '108']}; {'id': '92', 'type': 'boolean_operator', 'children': ['93', '100'], 'value': 'and'}; {'id': '93', 'type': 'call', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '95', 'type': 'argument_list', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'six'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'string_types'}; {'id': '100', 'type': 'comparison_operator', 'children': ['101', '107'], 'value': '>='}; {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'string', 'children': [], 'value': '":"'}; {'id': '107', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '108', 'type': 'block', 'children': ['109', '120']}; {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '114']}; {'id': '111', 'type': 'pattern_list', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'coords'}; {'id': '114', 'type': 'call', 'children': ['115', '118']}; {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}; {'id': '119', 'type': 'string', 'children': [], 'value': '":"'}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}; {'id': '121', 'type': 'assignment', 'children': ['122', '125']}; {'id': '122', 'type': 'pattern_list', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '125', 'type': 'list_comprehension', 'children': ['126', '130']}; {'id': '126', 'type': 'call', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '130', 'type': 'for_in_clause', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '132', 'type': 'call', 'children': ['133', '136']}; {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'coords'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}; {'id': '137', 'type': 'string', 'children': [], 'value': '"-"'}; {'id': '138', 'type': 'else_clause', 'children': ['139']}; {'id': '139', 'type': 'block', 'children': ['140', '144']}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}; {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}; {'id': '145', 'type': 'assignment', 'children': ['146', '149']}; {'id': '146', 'type': 'pattern_list', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '149', 'type': 'expression_list', 'children': ['150', '151']}; {'id': '150', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '151', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}; {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'sitems'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'tuple', 'children': ['159', '165', '166']}; {'id': '159', 'type': 'tuple', 'children': ['160', '163', '164']}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'contig_order'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'fname'}; {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'call', 'children': ['169', '172']}; {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'added_fnames'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '172', 'type': 'argument_list', 'children': ['173']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'fname'}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}; {'id': '175', 'type': 'call', 'children': ['176', '179']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'sitems'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '179', 'type': 'argument_list', 'children': []}; {'id': '180', 'type': 'return_statement', 'children': ['181']}; {'id': '181', 'type': 'list_comprehension', 'children': ['182', '189']}; {'id': '182', 'type': 'tuple', 'children': ['183', '186']}; {'id': '183', 'type': 'subscript', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '185', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '186', 'type': 'subscript', 'children': ['187', '188']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '188', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '189', 'type': 'for_in_clause', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'sitems'} | def _sort_by_region(fnames, regions, ref_file, config):
contig_order = {}
for i, sq in enumerate(ref.file_contigs(ref_file, config)):
contig_order[sq.name] = i
sitems = []
assert len(regions) == len(fnames), (regions, fnames)
added_fnames = set([])
for region, fname in zip(regions, fnames):
if fname not in added_fnames:
if isinstance(region, (list, tuple)):
c, s, e = region
elif isinstance(region, six.string_types) and region.find(":") >= 0:
c, coords = region.split(":")
s, e = [int(x) for x in coords.split("-")]
else:
c = region
s, e = 0, 0
sitems.append(((contig_order[c], s, e), c, fname))
added_fnames.add(fname)
sitems.sort()
return [(x[1], x[2]) for x in sitems] |
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{'id': '30', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'sorted_files'}; {'id': '32', 'type': 'if_clause', 'children': ['33']}; {'id': '33', 'type': 'boolean_operator', 'children': ['34', '42'], 'value': 'and'}; {'id': '34', 'type': 'call', 'children': ['35', '40']}; {'id': '35', 'type': 'attribute', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '42', 'type': 'call', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'vcf_has_variants'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '46', 'type': 'if_statement', 'children': ['47', '53', '73', '90']}; {'id': '47', 'type': 'comparison_operator', 'children': ['48', '52'], 'value': '=='}; {'id': '48', 'type': 'call', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'exist_files'}; {'id': '52', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '53', 'type': 'block', 'children': ['54']}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}; {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'exist_files'}; {'id': '57', 'type': 'list_comprehension', 'children': ['58', '59', '64']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '59', 'type': 'for_in_clause', 'children': ['60', '63']}; {'id': '60', 'type': 'pattern_list', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'sorted_files'}; {'id': '64', 'type': 'if_clause', 'children': ['65']}; {'id': '65', 'type': 'call', 'children': ['66', '71']}; {'id': '66', 'type': 'attribute', 'children': ['67', '70']}; {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'exists'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '73', 'type': 'elif_clause', 'children': ['74', '80']}; {'id': '74', 'type': 'comparison_operator', 'children': ['75', '79'], 'value': '>'}; {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'exist_files'}; {'id': '79', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '80', 'type': 'block', 'children': ['81']}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'exist_files'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': '_fix_gatk_header'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '88', '89']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'exist_files'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '90', 'type': 'else_clause', 'children': ['91']}; {'id': '91', 'type': 'block', 'children': ['92']}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}; {'id': '93', 'type': 'assignment', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'exist_files'}; {'id': '95', 'type': 'list_comprehension', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '97', 'type': 'for_in_clause', 'children': ['98', '101']}; {'id': '98', 'type': 'pattern_list', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'exist_files'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'ready_files'}; {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'run_multicore'}; {'id': '107', 'type': 'argument_list', 'children': ['108', '109', '116']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'p_bgzip_and_index'}; {'id': '109', 'type': 'list_comprehension', 'children': ['110', '113']}; {'id': '110', 'type': 'list', 'children': ['111', '112'], 'value': '[x, config]'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '113', 'type': 'for_in_clause', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'exist_files'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'input_file_list'}; {'id': '120', 'type': 'binary_operator', 'children': ['121', '122'], 'value': '%'}; {'id': '121', 'type': 'string', 'children': [], 'value': '"%s-files.list"'}; {'id': '122', 'type': 'subscript', 'children': ['123', '129']}; {'id': '123', 'type': 'call', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '129', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '130', 'type': 'with_statement', 'children': ['131', '141']}; {'id': '131', 'type': 'with_clause', 'children': ['132']}; {'id': '132', 'type': 'with_item', 'children': ['133']}; {'id': '133', 'type': 'as_pattern', 'children': ['134', '139']}; {'id': '134', 'type': 'call', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '136', 'type': 'argument_list', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'input_file_list'}; {'id': '138', 'type': 'string', 'children': [], 'value': '"w"'}; {'id': '139', 'type': 'as_pattern_target', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '141', 'type': 'block', 'children': ['142']}; {'id': '142', 'type': 'for_statement', 'children': ['143', '144', '145']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'fname'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'ready_files'}; {'id': '145', 'type': 'block', 'children': ['146']}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '151', 'type': 'argument_list', 'children': ['152']}; {'id': '152', 'type': 'binary_operator', 'children': ['153', '154'], 'value': '+'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'fname'}; {'id': '154', 'type': 'string', 'children': [], 'value': '"\\n"'}; {'id': '155', 'type': 'return_statement', 'children': ['156']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'input_file_list'} | def _get_file_list(orig_files, out_file, regions, ref_file, config):
sorted_files = _sort_by_region(orig_files, regions, ref_file, config)
exist_files = [(c, x) for c, x in sorted_files if os.path.exists(x) and vcf_has_variants(x)]
if len(exist_files) == 0:
exist_files = [x for c, x in sorted_files if os.path.exists(x)]
elif len(exist_files) > 1:
exist_files = _fix_gatk_header(exist_files, out_file, config)
else:
exist_files = [x for c, x in exist_files]
ready_files = run_multicore(p_bgzip_and_index, [[x, config] for x in exist_files], config)
input_file_list = "%s-files.list" % utils.splitext_plus(out_file)[0]
with open(input_file_list, "w") as out_handle:
for fname in ready_files:
out_handle.write(fname + "\n")
return input_file_list |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_by_ref'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'vcf_file'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '6', 'type': 'block', 'children': ['7', '20', '148']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '10', 'type': 'binary_operator', 'children': ['11', '12'], 'value': '%'}; {'id': '11', 'type': 'string', 'children': [], 'value': '"%s-prep.vcf.gz"'}; {'id': '12', 'type': 'subscript', 'children': ['13', '19']}; {'id': '13', 'type': 'call', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '17', 'type': 'argument_list', 'children': ['18']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'vcf_file'}; {'id': '19', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '20', 'type': 'if_statement', 'children': ['21', '29']}; {'id': '21', 'type': 'not_operator', 'children': ['22']}; {'id': '22', 'type': 'call', 'children': ['23', '26']}; {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'file_uptodate'}; {'id': '26', 'type': 'argument_list', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'vcf_file'}; {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'with_statement', 'children': ['31', '41']}; {'id': '31', 'type': 'with_clause', 'children': ['32']}; {'id': '32', 'type': 'with_item', 'children': ['33']}; {'id': '33', 'type': 'as_pattern', 'children': ['34', '39']}; {'id': '34', 'type': 'call', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'file_transaction'}; {'id': '36', 'type': 'argument_list', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '39', 'type': 'as_pattern_target', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '41', 'type': 'block', 'children': ['42', '55', '115']}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'header_file'}; {'id': '45', 'type': 'binary_operator', 'children': ['46', '47'], 'value': '%'}; {'id': '46', 'type': 'string', 'children': [], 'value': '"%s-header.txt"'}; {'id': '47', 'type': 'subscript', 'children': ['48', '54']}; {'id': '48', 'type': 'call', 'children': ['49', '52']}; {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'splitext_plus'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '54', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '55', 'type': 'with_statement', 'children': ['56', '66']}; {'id': '56', 'type': 'with_clause', 'children': ['57']}; {'id': '57', 'type': 'with_item', 'children': ['58']}; {'id': '58', 'type': 'as_pattern', 'children': ['59', '64']}; {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '61', 'type': 'argument_list', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'header_file'}; {'id': '63', 'type': 'string', 'children': [], 'value': '"w"'}; {'id': '64', 'type': 'as_pattern_target', 'children': ['65']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '66', 'type': 'block', 'children': ['67']}; {'id': '67', 'type': 'for_statement', 'children': ['68', '69', '83']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '69', 'type': 'call', 'children': ['70', '73']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'file_contigs'}; {'id': '73', 'type': 'argument_list', 'children': ['74', '80']}; {'id': '74', 'type': 'call', 'children': ['75', '78']}; {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'get_ref_file'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '80', 'type': 'subscript', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '82', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '83', 'type': 'block', 'children': ['84']}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}; {'id': '85', 'type': 'call', 'children': ['86', '89']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'out_handle'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '89', 'type': 'argument_list', 'children': ['90', '107']}; {'id': '90', 'type': 'ERROR', 'children': ['91', '100', '105']}; {'id': '91', 'type': 'attribute', 'children': ['92', '97', '99']}; {'id': '92', 'type': 'concatenated_string', 'children': ['93', '94', '96']}; {'id': '93', 'type': 'string', 'children': [], 'value': '"\n cat_cmd = "'}; {'id': '94', 'type': 'ERROR', 'children': ['95']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'zcat'}; {'id': '96', 'type': 'string', 'children': [], 'value': '" if vcf_file.endswith("'}; {'id': '97', 'type': 'ERROR', 'children': ['98']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'vcf'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'gz'}; {'id': '100', 'type': 'concatenated_string', 'children': ['101', '102', '104']}; {'id': '101', 'type': 'string', 'children': [], 'value': '") else "'}; {'id': '102', 'type': 'ERROR', 'children': ['103']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '104', 'type': 'string', 'children': [], 'value': '"\n cmd = ("'}; {'id': '105', 'type': 'set', 'children': ['106']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'cat_cmd'}; {'id': '107', 'type': 'binary_operator', 'children': ['108', '110'], 'value': '|'}; {'id': '108', 'type': 'set', 'children': ['109']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'vcf_file'}; {'id': '110', 'type': 'binary_operator', 'children': ['111', '114'], 'value': '^'}; {'id': '111', 'type': 'binary_operator', 'children': ['112', '113'], 'value': '-'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'grep'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '114', 'type': 'string', 'children': [], 'value': '"vt sort -m full -o {tx_out_file} -"'}; {'id': '115', 'type': 'with_statement', 'children': ['116', '131']}; {'id': '116', 'type': 'with_clause', 'children': ['117']}; {'id': '117', 'type': 'with_item', 'children': ['118']}; {'id': '118', 'type': 'call', 'children': ['119', '122']}; {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'chdir'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}; {'id': '123', 'type': 'call', 'children': ['124', '129']}; {'id': '124', 'type': 'attribute', 'children': ['125', '128']}; {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'dirname'}; {'id': '129', 'type': 'argument_list', 'children': ['130']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'tx_out_file'}; {'id': '131', 'type': 'block', 'children': ['132']}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}; {'id': '133', 'type': 'call', 'children': ['134', '137']}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'do'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '137', 'type': 'argument_list', 'children': ['138', '147']}; {'id': '138', 'type': 'call', 'children': ['139', '142']}; {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}; {'id': '143', 'type': 'dictionary_splat', 'children': ['144']}; {'id': '144', 'type': 'call', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '146', 'type': 'argument_list', 'children': []}; {'id': '147', 'type': 'string', 'children': [], 'value': '"Sort VCF by reference"'}; {'id': '148', 'type': 'return_statement', 'children': ['149']}; {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'bgzip_and_index'}; {'id': '151', 'type': 'argument_list', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '153', 'type': 'subscript', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '155', 'type': 'string', 'children': [], 'value': '"config"'} | def sort_by_ref(vcf_file, data):
out_file = "%s-prep.vcf.gz" % utils.splitext_plus(vcf_file)[0]
if not utils.file_uptodate(out_file, vcf_file):
with file_transaction(data, out_file) as tx_out_file:
header_file = "%s-header.txt" % utils.splitext_plus(tx_out_file)[0]
with open(header_file, "w") as out_handle:
for region in ref.file_contigs(dd.get_ref_file(data), data["config"]):
out_handle.write("
cat_cmd = "zcat" if vcf_file.endswith("vcf.gz") else "cat"
cmd = ("{cat_cmd} {vcf_file} | grep -v ^
"vt sort -m full -o {tx_out_file} -")
with utils.chdir(os.path.dirname(tx_out_file)):
do.run(cmd.format(**locals()), "Sort VCF by reference")
return bgzip_and_index(out_file, data["config"]) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'align_to_sort_bam'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'fastq1'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'fastq2'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'aligner'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '8', 'type': 'block', 'children': ['9', '15', '28', '47', '55', '72', '85', '122', '211']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '12', 'type': 'subscript', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '14', 'type': 'string', 'children': [], 'value': '"rgnames"'}; {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'align_dir_parts'}; {'id': '18', 'type': 'list', 'children': ['19', '24', '25'], 'value': '[data["dirs"]["work"], "align", names["sample"]]'}; {'id': '19', 'type': 'subscript', 'children': ['20', '23']}; {'id': '20', 'type': 'subscript', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '22', 'type': 'string', 'children': [], 'value': '"dirs"'}; {'id': '23', 'type': 'string', 'children': [], 'value': '"work"'}; {'id': '24', 'type': 'string', 'children': [], 'value': '"align"'}; {'id': '25', 'type': 'subscript', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '27', 'type': 'string', 'children': [], 'value': '"sample"'}; {'id': '28', 'type': 'if_statement', 'children': ['29', '35']}; {'id': '29', 'type': 'call', 'children': ['30', '33']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'string', 'children': [], 'value': '"disambiguate"'}; {'id': '35', 'type': 'block', 'children': ['36']}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}; {'id': '37', 'type': 'call', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'align_dir_parts'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'subscript', 'children': ['43', '46']}; {'id': '43', 'type': 'subscript', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '45', 'type': 'string', 'children': [], 'value': '"disambiguate"'}; {'id': '46', 'type': 'string', 'children': [], 'value': '"genome_build"'}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'aligner_index'}; {'id': '50', 'type': 'call', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': '_get_aligner_index'}; {'id': '52', 'type': 'argument_list', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'aligner'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'align_dir'}; {'id': '58', 'type': 'call', 'children': ['59', '62']}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'safe_makedir'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}; {'id': '63', 'type': 'call', 'children': ['64', '69']}; {'id': '64', 'type': 'attribute', 'children': ['65', '68']}; {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'list_splat', 'children': ['71']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'align_dir_parts'}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}; {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'tz'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'get_in'}; {'id': '79', 'type': 'argument_list', 'children': ['80', '84']}; {'id': '80', 'type': 'tuple', 'children': ['81', '82', '83']}; {'id': '81', 'type': 'string', 'children': [], 'value': '"reference"'}; {'id': '82', 'type': 'string', 'children': [], 'value': '"fasta"'}; {'id': '83', 'type': 'string', 'children': [], 'value': '"base"'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '85', 'type': 'if_statement', 'children': ['86', '92', '106']}; {'id': '86', 'type': 'call', 'children': ['87', '90']}; {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'fastq1'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}; {'id': '91', 'type': 'string', 'children': [], 'value': '".bam"'}; {'id': '92', 'type': 'block', 'children': ['93']}; {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '96', 'type': 'call', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': '_align_from_bam'}; {'id': '98', 'type': 'argument_list', 'children': ['99', '100', '101', '102', '103', '104', '105']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'fastq1'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'aligner'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'aligner_index'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'align_dir'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '106', 'type': 'else_clause', 'children': ['107']}; {'id': '107', 'type': 'block', 'children': ['108']}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}; {'id': '109', 'type': 'assignment', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '111', 'type': 'call', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': '_align_from_fastq'}; {'id': '113', 'type': 'argument_list', 'children': ['114', '115', '116', '117', '118', '119', '120', '121']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'fastq1'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'fastq2'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'aligner'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'aligner_index'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'align_dir'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '122', 'type': 'if_statement', 'children': ['123', '135']}; {'id': '123', 'type': 'boolean_operator', 'children': ['124', '127'], 'value': 'and'}; {'id': '124', 'type': 'subscript', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '126', 'type': 'string', 'children': [], 'value': '"work_bam"'}; {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'subscript', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '134', 'type': 'string', 'children': [], 'value': '"work_bam"'}; {'id': '135', 'type': 'block', 'children': ['136', '175']}; {'id': '136', 'type': 'if_statement', 'children': ['137', '150', '161']}; {'id': '137', 'type': 'boolean_operator', 'children': ['138', '144'], 'value': 'and'}; {'id': '138', 'type': 'call', 'children': ['139', '142']}; {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}; {'id': '143', 'type': 'string', 'children': [], 'value': '"align_split"'}; {'id': '144', 'type': 'call', 'children': ['145', '148']}; {'id': '145', 'type': 'attribute', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'get_mark_duplicates'}; {'id': '148', 'type': 'argument_list', 'children': ['149']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '150', 'type': 'block', 'children': ['151']}; {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'call', 'children': ['153', '156']}; {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'bam'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'fake_index'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '160']}; {'id': '157', 'type': 'subscript', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '159', 'type': 'string', 'children': [], 'value': '"work_bam"'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '161', 'type': 'else_clause', 'children': ['162']}; {'id': '162', 'type': 'block', 'children': ['163']}; {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '168']}; {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'bam'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '168', 'type': 'argument_list', 'children': ['169', '172']}; {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '171', 'type': 'string', 'children': [], 'value': '"work_bam"'}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '174', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '175', 'type': 'for_statement', 'children': ['176', '177', '180']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'extra'}; {'id': '177', 'type': 'list', 'children': ['178', '179'], 'value': '["-sr", "-disc"]'}; {'id': '178', 'type': 'string', 'children': [], 'value': '"-sr"'}; {'id': '179', 'type': 'string', 'children': [], 'value': '"-disc"'}; {'id': '180', 'type': 'block', 'children': ['181', '193']}; {'id': '181', 'type': 'expression_statement', 'children': ['182']}; {'id': '182', 'type': 'assignment', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'extra_bam'}; {'id': '184', 'type': 'call', 'children': ['185', '188']}; {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'append_stem'}; {'id': '188', 'type': 'argument_list', 'children': ['189', '192']}; {'id': '189', 'type': 'subscript', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '191', 'type': 'string', 'children': [], 'value': "'work_bam'"}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'extra'}; {'id': '193', 'type': 'if_statement', 'children': ['194', '200']}; {'id': '194', 'type': 'call', 'children': ['195', '198']}; {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '198', 'type': 'argument_list', 'children': ['199']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'extra_bam'}; {'id': '200', 'type': 'block', 'children': ['201']}; {'id': '201', 'type': 'expression_statement', 'children': ['202']}; {'id': '202', 'type': 'call', 'children': ['203', '206']}; {'id': '203', 'type': 'attribute', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'bam'}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '206', 'type': 'argument_list', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'extra_bam'}; {'id': '208', 'type': 'subscript', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '210', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '211', 'type': 'return_statement', 'children': ['212']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'data'} | def align_to_sort_bam(fastq1, fastq2, aligner, data):
names = data["rgnames"]
align_dir_parts = [data["dirs"]["work"], "align", names["sample"]]
if data.get("disambiguate"):
align_dir_parts.append(data["disambiguate"]["genome_build"])
aligner_index = _get_aligner_index(aligner, data)
align_dir = utils.safe_makedir(os.path.join(*align_dir_parts))
ref_file = tz.get_in(("reference", "fasta", "base"), data)
if fastq1.endswith(".bam"):
data = _align_from_bam(fastq1, aligner, aligner_index, ref_file,
names, align_dir, data)
else:
data = _align_from_fastq(fastq1, fastq2, aligner, aligner_index, ref_file,
names, align_dir, data)
if data["work_bam"] and utils.file_exists(data["work_bam"]):
if data.get("align_split") and dd.get_mark_duplicates(data):
bam.fake_index(data["work_bam"], data)
else:
bam.index(data["work_bam"], data["config"])
for extra in ["-sr", "-disc"]:
extra_bam = utils.append_stem(data['work_bam'], extra)
if utils.file_exists(extra_bam):
bam.index(extra_bam, data["config"])
return data |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_align_from_fastq'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '10', '11']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'fastq1'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'fastq2'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'aligner'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'align_ref'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'sam_ref'}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'align_dir'}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '12', 'type': 'block', 'children': ['13', '19', '27', '39']}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '16', 'type': 'subscript', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '18', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'align_fn'}; {'id': '22', 'type': 'attribute', 'children': ['23', '26']}; {'id': '23', 'type': 'subscript', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'TOOLS'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'aligner'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'align_fn'}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '30', 'type': 'call', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'align_fn'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '34', '35', '36', '37', '38']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'fastq1'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'fastq2'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'align_ref'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'align_dir'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '39', 'type': 'if_statement', 'children': ['40', '45', '68']}; {'id': '40', 'type': 'call', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '42', 'type': 'argument_list', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '45', 'type': 'block', 'children': ['46', '66']}; {'id': '46', 'type': 'assert_statement', 'children': ['47', '53']}; {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'string', 'children': [], 'value': '"work_bam"'}; {'id': '53', 'type': 'tuple', 'children': ['54', '60']}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'get_sample_name'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '60', 'type': 'call', 'children': ['61', '64']}; {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'string', 'children': [], 'value': '"work_bam"'}; {'id': '66', 'type': 'return_statement', 'children': ['67']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '68', 'type': 'else_clause', 'children': ['69']}; {'id': '69', 'type': 'block', 'children': ['70', '80', '92']}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}; {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'work_bam'}; {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'bam'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'sam_to_bam'}; {'id': '77', 'type': 'argument_list', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'assignment', 'children': ['82', '85']}; {'id': '82', 'type': 'subscript', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '84', 'type': 'string', 'children': [], 'value': '"work_bam"'}; {'id': '85', 'type': 'call', 'children': ['86', '89']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'bam'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '89', 'type': 'argument_list', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'work_bam'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '92', 'type': 'return_statement', 'children': ['93']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'data'} | def _align_from_fastq(fastq1, fastq2, aligner, align_ref, sam_ref, names,
align_dir, data):
config = data["config"]
align_fn = TOOLS[aligner].align_fn
out = align_fn(fastq1, fastq2, align_ref, names, align_dir, data)
if isinstance(out, dict):
assert out.get("work_bam"), (dd.get_sample_name(data), out.get("work_bam"))
return out
else:
work_bam = bam.sam_to_bam(out, config)
data["work_bam"] = bam.sort(work_bam, config)
return data |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'picard_prep'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'dirs'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '9', 'type': 'block', 'children': ['10', '22', '44', '52', '82', '110', '122', '133']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}; {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'runner'}; {'id': '13', 'type': 'call', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'broad'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'runner_from_path'}; {'id': '17', 'type': 'argument_list', 'children': ['18', '19']}; {'id': '18', 'type': 'string', 'children': [], 'value': '"picard"'}; {'id': '19', 'type': 'subscript', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '21', 'type': 'string', 'children': [], 'value': '"config"'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'work_dir'}; {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'safe_makedir'}; {'id': '29', 'type': 'argument_list', 'children': ['30']}; {'id': '30', 'type': 'call', 'children': ['31', '36']}; {'id': '31', 'type': 'attribute', 'children': ['32', '35']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '36', 'type': 'argument_list', 'children': ['37', '40', '41']}; {'id': '37', 'type': 'subscript', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'dirs'}; {'id': '39', 'type': 'string', 'children': [], 'value': '"work"'}; {'id': '40', 'type': 'string', 'children': [], 'value': '"bamclean"'}; {'id': '41', 'type': 'subscript', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '43', 'type': 'string', 'children': [], 'value': '"sample"'}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'runner'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'run_fn'}; {'id': '49', 'type': 'argument_list', 'children': ['50', '51']}; {'id': '50', 'type': 'string', 'children': [], 'value': '"picard_index_ref"'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}; {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'reorder_bam'}; {'id': '55', 'type': 'call', 'children': ['56', '61']}; {'id': '56', 'type': 'attribute', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '61', 'type': 'argument_list', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'work_dir'}; {'id': '63', 'type': 'binary_operator', 'children': ['64', '65'], 'value': '%'}; {'id': '64', 'type': 'string', 'children': [], 'value': '"%s-reorder.bam"'}; {'id': '65', 'type': 'subscript', 'children': ['66', '81']}; {'id': '66', 'type': 'call', 'children': ['67', '72']}; {'id': '67', 'type': 'attribute', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'splitext'}; {'id': '72', 'type': 'argument_list', 'children': ['73']}; {'id': '73', 'type': 'call', 'children': ['74', '79']}; {'id': '74', 'type': 'attribute', 'children': ['75', '78']}; {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '81', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '82', 'type': 'if_statement', 'children': ['83', '90']}; {'id': '83', 'type': 'not_operator', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}; {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'file_exists'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'reorder_bam'}; {'id': '90', 'type': 'block', 'children': ['91']}; {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'reorder_bam'}; {'id': '94', 'type': 'call', 'children': ['95', '100']}; {'id': '95', 'type': 'attribute', 'children': ['96', '99']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '100', 'type': 'argument_list', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'work_dir'}; {'id': '102', 'type': 'binary_operator', 'children': ['103', '104'], 'value': '%'}; {'id': '103', 'type': 'string', 'children': [], 'value': '"%s-reorder.bam"'}; {'id': '104', 'type': 'call', 'children': ['105', '108']}; {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'dd'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'get_sample_name'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}; {'id': '111', 'type': 'assignment', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'reorder_bam'}; {'id': '113', 'type': 'call', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'runner'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'run_fn'}; {'id': '117', 'type': 'argument_list', 'children': ['118', '119', '120', '121']}; {'id': '118', 'type': 'string', 'children': [], 'value': '"picard_reorder"'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'in_bam'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'reorder_bam'}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'rg_bam'}; {'id': '125', 'type': 'call', 'children': ['126', '129']}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'runner'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'run_fn'}; {'id': '129', 'type': 'argument_list', 'children': ['130', '131', '132']}; {'id': '130', 'type': 'string', 'children': [], 'value': '"picard_fix_rgs"'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'reorder_bam'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '133', 'type': 'return_statement', 'children': ['134']}; {'id': '134', 'type': 'call', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': '_filter_bad_reads'}; {'id': '136', 'type': 'argument_list', 'children': ['137', '138', '139']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'rg_bam'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'ref_file'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'data'} | def picard_prep(in_bam, names, ref_file, dirs, data):
runner = broad.runner_from_path("picard", data["config"])
work_dir = utils.safe_makedir(os.path.join(dirs["work"], "bamclean", names["sample"]))
runner.run_fn("picard_index_ref", ref_file)
reorder_bam = os.path.join(work_dir, "%s-reorder.bam" %
os.path.splitext(os.path.basename(in_bam))[0])
if not utils.file_exists(reorder_bam):
reorder_bam = os.path.join(work_dir, "%s-reorder.bam" % dd.get_sample_name(data))
reorder_bam = runner.run_fn("picard_reorder", in_bam, ref_file, reorder_bam)
rg_bam = runner.run_fn("picard_fix_rgs", reorder_bam, names)
return _filter_bad_reads(rg_bam, ref_file, data) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'iterate_flattened_separately'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'manually_sorted_keys'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '18', '34', '65', '79', '108']}; {'id': '9', 'type': 'if_statement', 'children': ['10', '13']}; {'id': '10', 'type': 'comparison_operator', 'children': ['11', '12'], 'value': 'is'}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'manually_sorted_keys'}; {'id': '12', 'type': 'None', 'children': []}; {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}; {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'manually_sorted_keys'}; {'id': '17', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '18', 'type': 'for_statement', 'children': ['19', '20', '21']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'manually_sorted_keys'}; {'id': '21', 'type': 'block', 'children': ['22']}; {'id': '22', 'type': 'if_statement', 'children': ['23', '26']}; {'id': '23', 'type': 'comparison_operator', 'children': ['24', '25'], 'value': 'in'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '26', 'type': 'block', 'children': ['27']}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'yield', 'children': ['29']}; {'id': '29', 'type': 'expression_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '31', 'type': 'subscript', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}; {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'single_line_keys'}; {'id': '37', 'type': 'list_comprehension', 'children': ['38', '39', '46']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '39', 'type': 'for_in_clause', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '45', 'type': 'argument_list', 'children': []}; {'id': '46', 'type': 'if_clause', 'children': ['47']}; {'id': '47', 'type': 'boolean_operator', 'children': ['48', '51'], 'value': 'and'}; {'id': '48', 'type': 'comparison_operator', 'children': ['49', '50'], 'value': 'not'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'manually_sorted_keys'}; {'id': '51', 'type': '()', 'children': ['52']}; {'id': '52', 'type': 'boolean_operator', 'children': ['53', '57'], 'value': 'or'}; {'id': '53', 'type': 'not_operator', 'children': ['54']}; {'id': '54', 'type': 'subscript', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '57', 'type': 'not_operator', 'children': ['58']}; {'id': '58', 'type': 'call', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '60', 'type': 'argument_list', 'children': ['61', '64']}; {'id': '61', 'type': 'subscript', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '65', 'type': 'for_statement', 'children': ['66', '67', '71']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'single_line_keys'}; {'id': '71', 'type': 'block', 'children': ['72']}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}; {'id': '73', 'type': 'yield', 'children': ['74']}; {'id': '74', 'type': 'expression_list', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '76', 'type': 'subscript', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'multi_line_keys'}; {'id': '82', 'type': 'list_comprehension', 'children': ['83', '84', '91']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '84', 'type': 'for_in_clause', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '86', 'type': 'call', 'children': ['87', '90']}; {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '90', 'type': 'argument_list', 'children': []}; {'id': '91', 'type': 'if_clause', 'children': ['92']}; {'id': '92', 'type': 'boolean_operator', 'children': ['93', '96'], 'value': 'and'}; {'id': '93', 'type': 'comparison_operator', 'children': ['94', '95'], 'value': 'not'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'manually_sorted_keys'}; {'id': '96', 'type': '()', 'children': ['97']}; {'id': '97', 'type': 'boolean_operator', 'children': ['98', '101'], 'value': 'and'}; {'id': '98', 'type': 'subscript', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '101', 'type': 'call', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '103', 'type': 'argument_list', 'children': ['104', '107']}; {'id': '104', 'type': 'subscript', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '108', 'type': 'for_statement', 'children': ['109', '110', '114']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '110', 'type': 'call', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'multi_line_keys'}; {'id': '114', 'type': 'block', 'children': ['115', '120']}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'yield', 'children': ['117']}; {'id': '117', 'type': 'expression_list', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'PATHCHANGE'}; {'id': '120', 'type': 'for_statement', 'children': ['121', '124', '131']}; {'id': '121', 'type': 'pattern_list', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '124', 'type': 'call', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'iterate_flattened_separately'}; {'id': '126', 'type': 'argument_list', 'children': ['127', '130']}; {'id': '127', 'type': 'subscript', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'dictionary'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'manually_sorted_keys'}; {'id': '131', 'type': 'block', 'children': ['132']}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}; {'id': '133', 'type': 'yield', 'children': ['134']}; {'id': '134', 'type': 'expression_list', 'children': ['135', '140']}; {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'join_paths'}; {'id': '137', 'type': 'argument_list', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'val'} | def iterate_flattened_separately(dictionary, manually_sorted_keys=None):
if manually_sorted_keys is None:
manually_sorted_keys = []
for key in manually_sorted_keys:
if key in dictionary:
yield key, dictionary[key]
single_line_keys = [key for key in dictionary.keys() if
key not in manually_sorted_keys and
(not dictionary[key] or
not isinstance(dictionary[key], dict))]
for key in sorted(single_line_keys):
yield key, dictionary[key]
multi_line_keys = [key for key in dictionary.keys() if
key not in manually_sorted_keys and
(dictionary[key] and
isinstance(dictionary[key], dict))]
for key in sorted(multi_line_keys):
yield key, PATHCHANGE
for k, val in iterate_flattened_separately(dictionary[key],
manually_sorted_keys):
yield join_paths(key, k), val |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'gather_command_line_options'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'default_parameter', 'children': ['5', '6']}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'filter_disabled'}; {'id': '6', 'type': 'None', 'children': []}; {'id': '7', 'type': 'block', 'children': ['8', '22', '40']}; {'id': '8', 'type': 'if_statement', 'children': ['9', '12']}; {'id': '9', 'type': 'comparison_operator', 'children': ['10', '11'], 'value': 'is'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'filter_disabled'}; {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'block', 'children': ['13']}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'filter_disabled'}; {'id': '16', 'type': 'not_operator', 'children': ['17']}; {'id': '17', 'type': 'attribute', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'SETTINGS'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'COMMAND_LINE'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'SHOW_DISABLED_OPTIONS'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '25', 'type': 'list_comprehension', 'children': ['26', '27', '33']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'opt'}; {'id': '27', 'type': 'for_in_clause', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'opt'}; {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'get_inheritors'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'CommandLineOption'}; {'id': '33', 'type': 'if_clause', 'children': ['34']}; {'id': '34', 'type': 'boolean_operator', 'children': ['35', '37'], 'value': 'or'}; {'id': '35', 'type': 'not_operator', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'filter_disabled'}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'opt'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': '_enabled'}; {'id': '40', 'type': 'return_statement', 'children': ['41']}; {'id': '41', 'type': 'call', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '43', 'type': 'argument_list', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '45', 'type': 'keyword_argument', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '47', 'type': 'lambda', 'children': ['48', '50']}; {'id': '48', 'type': 'lambda_parameters', 'children': ['49']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'opt'}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'opt'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': '__name__'} | def gather_command_line_options(filter_disabled=None):
if filter_disabled is None:
filter_disabled = not SETTINGS.COMMAND_LINE.SHOW_DISABLED_OPTIONS
options = [opt for opt in get_inheritors(CommandLineOption)
if not filter_disabled or opt._enabled]
return sorted(options, key=lambda opt: opt.__name__) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '37']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'bar'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '10', '13', '16', '19', '22', '25', '28', '31', '34']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'figsize'}; {'id': '7', 'type': 'tuple', 'children': ['8', '9']}; {'id': '8', 'type': 'integer', 'children': [], 'value': '24'}; {'id': '9', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '12', 'type': 'integer', 'children': [], 'value': '16'}; {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'default_parameter', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '18', 'type': 'False', 'children': []}; {'id': '19', 'type': 'default_parameter', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '21', 'type': 'string', 'children': [], 'value': "'dimgray'"}; {'id': '22', 'type': 'default_parameter', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'inline'}; {'id': '24', 'type': 'False', 'children': []}; {'id': '25', 'type': 'default_parameter', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '27', 'type': 'None', 'children': []}; {'id': '28', 'type': 'default_parameter', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '30', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '31', 'type': 'default_parameter', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '33', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '34', 'type': 'default_parameter', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '36', 'type': 'None', 'children': []}; {'id': '37', 'type': 'block', 'children': ['38', '55', '71', '81', '90', '117', '125', '130', '287', '295', '302', '313', '324', '342', '349', '415']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}; {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'nullity_counts'}; {'id': '41', 'type': 'binary_operator', 'children': ['42', '46'], 'value': '-'}; {'id': '42', 'type': 'call', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '46', 'type': 'call', 'children': ['47', '54']}; {'id': '47', 'type': 'attribute', 'children': ['48', '53']}; {'id': '48', 'type': 'call', 'children': ['49', '52']}; {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'isnull'}; {'id': '52', 'type': 'argument_list', 'children': []}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'sum'}; {'id': '54', 'type': 'argument_list', 'children': []}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '58', 'type': 'call', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'nullity_filter'}; {'id': '60', 'type': 'argument_list', 'children': ['61', '62', '65', '68']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '62', 'type': 'keyword_argument', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '65', 'type': 'keyword_argument', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '68', 'type': 'keyword_argument', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '74', 'type': 'call', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'nullity_sort'}; {'id': '76', 'type': 'argument_list', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '78', 'type': 'keyword_argument', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'figure'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'keyword_argument', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'figsize'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'figsize'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}; {'id': '91', 'type': 'call', 'children': ['92', '101']}; {'id': '92', 'type': 'attribute', 'children': ['93', '100']}; {'id': '93', 'type': '()', 'children': ['94']}; {'id': '94', 'type': 'binary_operator', 'children': ['95', '96'], 'value': '/'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'nullity_counts'}; {'id': '96', 'type': 'call', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'plot'}; {'id': '101', 'type': 'argument_list', 'children': ['102', '105', '108', '111', '114']}; {'id': '102', 'type': 'keyword_argument', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '104', 'type': 'string', 'children': [], 'value': "'bar'"}; {'id': '105', 'type': 'keyword_argument', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'figsize'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'figsize'}; {'id': '108', 'type': 'keyword_argument', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '111', 'type': 'keyword_argument', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '114', 'type': 'keyword_argument', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '120', 'type': 'call', 'children': ['121', '124']}; {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'gca'}; {'id': '124', 'type': 'argument_list', 'children': []}; {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'axes'}; {'id': '128', 'type': 'list', 'children': ['129'], 'value': '[ax1]'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '130', 'type': 'if_statement', 'children': ['131', '146', '278']}; {'id': '131', 'type': 'boolean_operator', 'children': ['132', '133'], 'value': 'or'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '133', 'type': '()', 'children': ['134']}; {'id': '134', 'type': 'boolean_operator', 'children': ['135', '138'], 'value': 'and'}; {'id': '135', 'type': 'comparison_operator', 'children': ['136', '137'], 'value': 'is'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '137', 'type': 'None', 'children': []}; {'id': '138', 'type': 'comparison_operator', 'children': ['139', '145'], 'value': '<='}; {'id': '139', 'type': 'call', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '141', 'type': 'argument_list', 'children': ['142']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '145', 'type': 'integer', 'children': [], 'value': '50'}; {'id': '146', 'type': 'block', 'children': ['147', '167', '175', '182']}; {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'call', 'children': ['149', '152']}; {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'set_xticklabels'}; {'id': '152', 'type': 'argument_list', 'children': ['153', '158', '161', '164']}; {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'get_xticklabels'}; {'id': '157', 'type': 'argument_list', 'children': []}; {'id': '158', 'type': 'keyword_argument', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'rotation'}; {'id': '160', 'type': 'integer', 'children': [], 'value': '45'}; {'id': '161', 'type': 'keyword_argument', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'ha'}; {'id': '163', 'type': 'string', 'children': [], 'value': "'right'"}; {'id': '164', 'type': 'keyword_argument', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'assignment', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'ax2'}; {'id': '170', 'type': 'call', 'children': ['171', '174']}; {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'twinx'}; {'id': '174', 'type': 'argument_list', 'children': []}; {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'call', 'children': ['177', '180']}; {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'axes'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '180', 'type': 'argument_list', 'children': ['181']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'ax2'}; {'id': '182', 'type': 'if_statement', 'children': ['183', '185', '232']}; {'id': '183', 'type': 'not_operator', 'children': ['184']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '185', 'type': 'block', 'children': ['186', '195', '206']}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}; {'id': '187', 'type': 'call', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'set_ylim'}; {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'list', 'children': ['193', '194'], 'value': '[0, 1]'}; {'id': '193', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '194', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'call', 'children': ['197', '200']}; {'id': '197', 'type': 'attribute', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'ax2'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'set_yticks'}; {'id': '200', 'type': 'argument_list', 'children': ['201']}; {'id': '201', 'type': 'call', 'children': ['202', '205']}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'get_yticks'}; {'id': '205', 'type': 'argument_list', 'children': []}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}; {'id': '207', 'type': 'call', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'ax2'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'set_yticklabels'}; {'id': '211', 'type': 'argument_list', 'children': ['212', '229']}; {'id': '212', 'type': 'list_comprehension', 'children': ['213', '222']}; {'id': '213', 'type': 'call', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '215', 'type': 'argument_list', 'children': ['216']}; {'id': '216', 'type': 'binary_operator', 'children': ['217', '218'], 'value': '*'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '218', 'type': 'call', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '220', 'type': 'argument_list', 'children': ['221']}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '222', 'type': 'for_in_clause', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '224', 'type': 'call', 'children': ['225', '228']}; {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'get_yticks'}; {'id': '228', 'type': 'argument_list', 'children': []}; {'id': '229', 'type': 'keyword_argument', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '232', 'type': 'else_clause', 'children': ['233']}; {'id': '233', 'type': 'block', 'children': ['234', '241', '252']}; {'id': '234', 'type': 'expression_statement', 'children': ['235']}; {'id': '235', 'type': 'call', 'children': ['236', '239']}; {'id': '236', 'type': 'attribute', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'ax2'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'set_yscale'}; {'id': '239', 'type': 'argument_list', 'children': ['240']}; {'id': '240', 'type': 'string', 'children': [], 'value': "'log'"}; {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'call', 'children': ['243', '246']}; {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'ax2'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'set_ylim'}; {'id': '246', 'type': 'argument_list', 'children': ['247']}; {'id': '247', 'type': 'call', 'children': ['248', '251']}; {'id': '248', 'type': 'attribute', 'children': ['249', '250']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'get_ylim'}; {'id': '251', 'type': 'argument_list', 'children': []}; {'id': '252', 'type': 'expression_statement', 'children': ['253']}; {'id': '253', 'type': 'call', 'children': ['254', '257']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'ax2'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'set_yticklabels'}; {'id': '257', 'type': 'argument_list', 'children': ['258', '275']}; {'id': '258', 'type': 'list_comprehension', 'children': ['259', '268']}; {'id': '259', 'type': 'call', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '261', 'type': 'argument_list', 'children': ['262']}; {'id': '262', 'type': 'binary_operator', 'children': ['263', '264'], 'value': '*'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '264', 'type': 'call', 'children': ['265', '266']}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '266', 'type': 'argument_list', 'children': ['267']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '268', 'type': 'for_in_clause', 'children': ['269', '270']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '270', 'type': 'call', 'children': ['271', '274']}; {'id': '271', 'type': 'attribute', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'get_yticks'}; {'id': '274', 'type': 'argument_list', 'children': []}; {'id': '275', 'type': 'keyword_argument', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '278', 'type': 'else_clause', 'children': ['279']}; {'id': '279', 'type': 'block', 'children': ['280']}; {'id': '280', 'type': 'expression_statement', 'children': ['281']}; {'id': '281', 'type': 'call', 'children': ['282', '285']}; {'id': '282', 'type': 'attribute', 'children': ['283', '284']}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'set_xticks'}; {'id': '285', 'type': 'argument_list', 'children': ['286']}; {'id': '286', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'assignment', 'children': ['289', '290']}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'ax3'}; {'id': '290', 'type': 'call', 'children': ['291', '294']}; {'id': '291', 'type': 'attribute', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'twiny'}; {'id': '294', 'type': 'argument_list', 'children': []}; {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'call', 'children': ['297', '300']}; {'id': '297', 'type': 'attribute', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'axes'}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '300', 'type': 'argument_list', 'children': ['301']}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'ax3'}; {'id': '302', 'type': 'expression_statement', 'children': ['303']}; {'id': '303', 'type': 'call', 'children': ['304', '307']}; {'id': '304', 'type': 'attribute', 'children': ['305', '306']}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'ax3'}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'set_xticks'}; {'id': '307', 'type': 'argument_list', 'children': ['308']}; {'id': '308', 'type': 'call', 'children': ['309', '312']}; {'id': '309', 'type': 'attribute', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '311', 'type': 'identifier', 'children': [], 'value': 'get_xticks'}; {'id': '312', 'type': 'argument_list', 'children': []}; {'id': '313', 'type': 'expression_statement', 'children': ['314']}; {'id': '314', 'type': 'call', 'children': ['315', '318']}; {'id': '315', 'type': 'attribute', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'ax3'}; {'id': '317', 'type': 'identifier', 'children': [], 'value': 'set_xlim'}; {'id': '318', 'type': 'argument_list', 'children': ['319']}; {'id': '319', 'type': 'call', 'children': ['320', '323']}; {'id': '320', 'type': 'attribute', 'children': ['321', '322']}; {'id': '321', 'type': 'identifier', 'children': [], 'value': 'ax1'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'get_xlim'}; {'id': '323', 'type': 'argument_list', 'children': []}; {'id': '324', 'type': 'expression_statement', 'children': ['325']}; {'id': '325', 'type': 'call', 'children': ['326', '329']}; {'id': '326', 'type': 'attribute', 'children': ['327', '328']}; {'id': '327', 'type': 'identifier', 'children': [], 'value': 'ax3'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'set_xticklabels'}; {'id': '329', 'type': 'argument_list', 'children': ['330', '333', '336', '339']}; {'id': '330', 'type': 'attribute', 'children': ['331', '332']}; {'id': '331', 'type': 'identifier', 'children': [], 'value': 'nullity_counts'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '333', 'type': 'keyword_argument', 'children': ['334', '335']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '335', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '336', 'type': 'keyword_argument', 'children': ['337', '338']}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 'rotation'}; {'id': '338', 'type': 'integer', 'children': [], 'value': '45'}; {'id': '339', 'type': 'keyword_argument', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'ha'}; {'id': '341', 'type': 'string', 'children': [], 'value': "'left'"}; {'id': '342', 'type': 'expression_statement', 'children': ['343']}; {'id': '343', 'type': 'call', 'children': ['344', '347']}; {'id': '344', 'type': 'attribute', 'children': ['345', '346']}; {'id': '345', 'type': 'identifier', 'children': [], 'value': 'ax3'}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'grid'}; {'id': '347', 'type': 'argument_list', 'children': ['348']}; {'id': '348', 'type': 'False', 'children': []}; {'id': '349', 'type': 'for_statement', 'children': ['350', '351', '352']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '351', 'type': 'identifier', 'children': [], 'value': 'axes'}; {'id': '352', 'type': 'block', 'children': ['353', '364', '375', '386', '397', '406']}; {'id': '353', 'type': 'expression_statement', 'children': ['354']}; {'id': '354', 'type': 'call', 'children': ['355', '362']}; {'id': '355', 'type': 'attribute', 'children': ['356', '361']}; {'id': '356', 'type': 'subscript', 'children': ['357', '360']}; {'id': '357', 'type': 'attribute', 'children': ['358', '359']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '359', 'type': 'identifier', 'children': [], 'value': 'spines'}; {'id': '360', 'type': 'string', 'children': [], 'value': "'top'"}; {'id': '361', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '362', 'type': 'argument_list', 'children': ['363']}; {'id': '363', 'type': 'False', 'children': []}; {'id': '364', 'type': 'expression_statement', 'children': ['365']}; {'id': '365', 'type': 'call', 'children': ['366', '373']}; {'id': '366', 'type': 'attribute', 'children': ['367', '372']}; {'id': '367', 'type': 'subscript', 'children': ['368', '371']}; {'id': '368', 'type': 'attribute', 'children': ['369', '370']}; {'id': '369', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'spines'}; {'id': '371', 'type': 'string', 'children': [], 'value': "'right'"}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '373', 'type': 'argument_list', 'children': ['374']}; {'id': '374', 'type': 'False', 'children': []}; {'id': '375', 'type': 'expression_statement', 'children': ['376']}; {'id': '376', 'type': 'call', 'children': ['377', '384']}; {'id': '377', 'type': 'attribute', 'children': ['378', '383']}; {'id': '378', 'type': 'subscript', 'children': ['379', '382']}; {'id': '379', 'type': 'attribute', 'children': ['380', '381']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '381', 'type': 'identifier', 'children': [], 'value': 'spines'}; {'id': '382', 'type': 'string', 'children': [], 'value': "'bottom'"}; {'id': '383', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '384', 'type': 'argument_list', 'children': ['385']}; {'id': '385', 'type': 'False', 'children': []}; {'id': '386', 'type': 'expression_statement', 'children': ['387']}; {'id': '387', 'type': 'call', 'children': ['388', '395']}; {'id': '388', 'type': 'attribute', 'children': ['389', '394']}; {'id': '389', 'type': 'subscript', 'children': ['390', '393']}; {'id': '390', 'type': 'attribute', 'children': ['391', '392']}; {'id': '391', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'spines'}; {'id': '393', 'type': 'string', 'children': [], 'value': "'left'"}; {'id': '394', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '395', 'type': 'argument_list', 'children': ['396']}; {'id': '396', 'type': 'False', 'children': []}; {'id': '397', 'type': 'expression_statement', 'children': ['398']}; {'id': '398', 'type': 'call', 'children': ['399', '404']}; {'id': '399', 'type': 'attribute', 'children': ['400', '403']}; {'id': '400', 'type': 'attribute', 'children': ['401', '402']}; {'id': '401', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '402', 'type': 'identifier', 'children': [], 'value': 'xaxis'}; {'id': '403', 'type': 'identifier', 'children': [], 'value': 'set_ticks_position'}; {'id': '404', 'type': 'argument_list', 'children': ['405']}; {'id': '405', 'type': 'string', 'children': [], 'value': "'none'"}; {'id': '406', 'type': 'expression_statement', 'children': ['407']}; {'id': '407', 'type': 'call', 'children': ['408', '413']}; {'id': '408', 'type': 'attribute', 'children': ['409', '412']}; {'id': '409', 'type': 'attribute', 'children': ['410', '411']}; {'id': '410', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '411', 'type': 'identifier', 'children': [], 'value': 'yaxis'}; {'id': '412', 'type': 'identifier', 'children': [], 'value': 'set_ticks_position'}; {'id': '413', 'type': 'argument_list', 'children': ['414']}; {'id': '414', 'type': 'string', 'children': [], 'value': "'none'"}; {'id': '415', 'type': 'if_statement', 'children': ['416', '417', '424']}; {'id': '416', 'type': 'identifier', 'children': [], 'value': 'inline'}; {'id': '417', 'type': 'block', 'children': ['418']}; {'id': '418', 'type': 'expression_statement', 'children': ['419']}; {'id': '419', 'type': 'call', 'children': ['420', '423']}; {'id': '420', 'type': 'attribute', 'children': ['421', '422']}; {'id': '421', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '422', 'type': 'identifier', 'children': [], 'value': 'show'}; {'id': '423', 'type': 'argument_list', 'children': []}; {'id': '424', 'type': 'else_clause', 'children': ['425']}; {'id': '425', 'type': 'block', 'children': ['426']}; {'id': '426', 'type': 'return_statement', 'children': ['427']}; {'id': '427', 'type': 'identifier', 'children': [], 'value': 'ax1'} | def bar(df, figsize=(24, 10), fontsize=16, labels=None, log=False, color='dimgray', inline=False,
filter=None, n=0, p=0, sort=None):
nullity_counts = len(df) - df.isnull().sum()
df = nullity_filter(df, filter=filter, n=n, p=p)
df = nullity_sort(df, sort=sort)
plt.figure(figsize=figsize)
(nullity_counts / len(df)).plot(kind='bar', figsize=figsize, fontsize=fontsize, log=log, color=color)
ax1 = plt.gca()
axes = [ax1]
if labels or (labels is None and len(df.columns) <= 50):
ax1.set_xticklabels(ax1.get_xticklabels(), rotation=45, ha='right', fontsize=fontsize)
ax2 = ax1.twinx()
axes.append(ax2)
if not log:
ax1.set_ylim([0, 1])
ax2.set_yticks(ax1.get_yticks())
ax2.set_yticklabels([int(n*len(df)) for n in ax1.get_yticks()], fontsize=fontsize)
else:
ax2.set_yscale('log')
ax2.set_ylim(ax1.get_ylim())
ax2.set_yticklabels([int(n*len(df)) for n in ax1.get_yticks()], fontsize=fontsize)
else:
ax1.set_xticks([])
ax3 = ax1.twiny()
axes.append(ax3)
ax3.set_xticks(ax1.get_xticks())
ax3.set_xlim(ax1.get_xlim())
ax3.set_xticklabels(nullity_counts.values, fontsize=fontsize, rotation=45, ha='left')
ax3.grid(False)
for ax in axes:
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
ax.spines['bottom'].set_visible(False)
ax.spines['left'].set_visible(False)
ax.xaxis.set_ticks_position('none')
ax.yaxis.set_ticks_position('none')
if inline:
plt.show()
else:
return ax1 |
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{'id': '15', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '16', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'figsize'}; {'id': '22', 'type': 'tuple', 'children': ['23', '24']}; {'id': '23', 'type': 'integer', 'children': [], 'value': '20'}; {'id': '24', 'type': 'integer', 'children': [], 'value': '12'}; {'id': '25', 'type': 'default_parameter', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '27', 'type': 'integer', 'children': [], 'value': '16'}; {'id': '28', 'type': 'default_parameter', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '30', 'type': 'True', 'children': []}; {'id': '31', 'type': 'default_parameter', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '33', 'type': 'string', 'children': [], 'value': "'RdBu'"}; {'id': '34', 'type': 'default_parameter', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'vmin'}; {'id': '36', 'type': 'unary_operator', 'children': ['37'], 'value': '-'}; {'id': '37', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '38', 'type': 'default_parameter', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'vmax'}; {'id': '40', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '41', 'type': 'default_parameter', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'cbar'}; {'id': '43', 'type': 'True', 'children': []}; {'id': '44', 'type': 'block', 'children': ['45', '61', '71', '80', '90', '101', '136', '148', '157', '168', '234', '242', '264', '283', '302', '311', '320', '329', '426']}; {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '48', 'type': 'call', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'nullity_filter'}; {'id': '50', 'type': 'argument_list', 'children': ['51', '52', '55', '58']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '52', 'type': 'keyword_argument', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '55', 'type': 'keyword_argument', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '58', 'type': 'keyword_argument', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '64', 'type': 'call', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'nullity_sort'}; {'id': '66', 'type': 'argument_list', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '68', 'type': 'keyword_argument', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'call', 'children': ['73', '76']}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'figure'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}; {'id': '77', 'type': 'keyword_argument', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'figsize'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'figsize'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'gs'}; {'id': '83', 'type': 'call', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'gridspec'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'GridSpec'}; {'id': '87', 'type': 'argument_list', 'children': ['88', '89']}; {'id': '88', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '89', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}; {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '93', 'type': 'call', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'subplot'}; {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'subscript', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'gs'}; {'id': '100', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '104', 'type': 'subscript', 'children': ['105', '108', '110']}; {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'iloc'}; {'id': '108', 'type': 'slice', 'children': ['109']}; {'id': '109', 'type': 'colon', 'children': []}; {'id': '110', 'type': 'list_comprehension', 'children': ['111', '112', '132']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '112', 'type': 'for_in_clause', 'children': ['113', '116']}; {'id': '113', 'type': 'pattern_list', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '116', 'type': 'call', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}; {'id': '119', 'type': 'call', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '123', 'type': 'argument_list', 'children': ['124', '129']}; {'id': '124', 'type': 'call', 'children': ['125', '128']}; {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'isnull'}; {'id': '128', 'type': 'argument_list', 'children': []}; {'id': '129', 'type': 'keyword_argument', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '131', 'type': 'string', 'children': [], 'value': "'rows'"}; {'id': '132', 'type': 'if_clause', 'children': ['133']}; {'id': '133', 'type': 'comparison_operator', 'children': ['134', '135'], 'value': '>'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '135', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}; {'id': '137', 'type': 'assignment', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'corr_mat'}; {'id': '139', 'type': 'call', 'children': ['140', '147']}; {'id': '140', 'type': 'attribute', 'children': ['141', '146']}; {'id': '141', 'type': 'call', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'isnull'}; {'id': '145', 'type': 'argument_list', 'children': []}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'corr'}; {'id': '147', 'type': 'argument_list', 'children': []}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}; {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'mask'}; {'id': '151', 'type': 'call', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'zeros_like'}; {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'corr_mat'}; {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '167']}; {'id': '159', 'type': 'subscript', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'mask'}; {'id': '161', 'type': 'call', 'children': ['162', '165']}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'triu_indices_from'}; {'id': '165', 'type': 'argument_list', 'children': ['166']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'mask'}; {'id': '167', 'type': 'True', 'children': []}; {'id': '168', 'type': 'if_statement', 'children': ['169', '170', '207']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '170', 'type': 'block', 'children': ['171']}; {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'call', 'children': ['173', '176']}; {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'sns'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'heatmap'}; {'id': '176', 'type': 'argument_list', 'children': ['177', '178', '181', '184', '187', '190', '193', '201', '204']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'corr_mat'}; {'id': '178', 'type': 'keyword_argument', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'mask'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'mask'}; {'id': '181', 'type': 'keyword_argument', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '184', 'type': 'keyword_argument', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '187', 'type': 'keyword_argument', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'cbar'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'cbar'}; {'id': '190', 'type': 'keyword_argument', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'annot'}; {'id': '192', 'type': 'True', 'children': []}; {'id': '193', 'type': 'keyword_argument', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'annot_kws'}; {'id': '195', 'type': 'dictionary', 'children': ['196']}; {'id': '196', 'type': 'pair', 'children': ['197', '198']}; {'id': '197', 'type': 'string', 'children': [], 'value': "'size'"}; {'id': '198', 'type': 'binary_operator', 'children': ['199', '200'], 'value': '-'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '200', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '201', 'type': 'keyword_argument', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'vmin'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'vmin'}; {'id': '204', 'type': 'keyword_argument', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'vmax'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'vmax'}; {'id': '207', 'type': 'else_clause', 'children': ['208']}; {'id': '208', 'type': 'block', 'children': ['209']}; {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'call', 'children': ['211', '214']}; {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'sns'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'heatmap'}; {'id': '214', 'type': 'argument_list', 'children': ['215', '216', '219', '222', '225', '228', '231']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'corr_mat'}; {'id': '216', 'type': 'keyword_argument', 'children': ['217', '218']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'mask'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'mask'}; {'id': '219', 'type': 'keyword_argument', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '222', 'type': 'keyword_argument', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '225', 'type': 'keyword_argument', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'cbar'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'cbar'}; {'id': '228', 'type': 'keyword_argument', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'vmin'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'vmin'}; {'id': '231', 'type': 'keyword_argument', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'vmax'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'vmax'}; {'id': '234', 'type': 'expression_statement', 'children': ['235']}; {'id': '235', 'type': 'call', 'children': ['236', '241']}; {'id': '236', 'type': 'attribute', 'children': ['237', '240']}; {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'xaxis'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'tick_bottom'}; {'id': '241', 'type': 'argument_list', 'children': []}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}; {'id': '243', 'type': 'call', 'children': ['244', '247']}; {'id': '244', 'type': 'attribute', 'children': ['245', '246']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'set_xticklabels'}; {'id': '247', 'type': 'argument_list', 'children': ['248', '255', '258', '261']}; {'id': '248', 'type': 'call', 'children': ['249', '254']}; {'id': '249', 'type': 'attribute', 'children': ['250', '253']}; {'id': '250', 'type': 'attribute', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'xaxis'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'get_majorticklabels'}; {'id': '254', 'type': 'argument_list', 'children': []}; {'id': '255', 'type': 'keyword_argument', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'rotation'}; {'id': '257', 'type': 'integer', 'children': [], 'value': '45'}; {'id': '258', 'type': 'keyword_argument', 'children': ['259', '260']}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'ha'}; {'id': '260', 'type': 'string', 'children': [], 'value': "'right'"}; {'id': '261', 'type': 'keyword_argument', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}; {'id': '265', 'type': 'call', 'children': ['266', '269']}; {'id': '266', 'type': 'attribute', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'set_yticklabels'}; {'id': '269', 'type': 'argument_list', 'children': ['270', '277', '280']}; {'id': '270', 'type': 'call', 'children': ['271', '276']}; {'id': '271', 'type': 'attribute', 'children': ['272', '275']}; {'id': '272', 'type': 'attribute', 'children': ['273', '274']}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'yaxis'}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'get_majorticklabels'}; {'id': '276', 'type': 'argument_list', 'children': []}; {'id': '277', 'type': 'keyword_argument', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '280', 'type': 'keyword_argument', 'children': ['281', '282']}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'rotation'}; {'id': '282', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '283', 'type': 'expression_statement', 'children': ['284']}; {'id': '284', 'type': 'call', 'children': ['285', '288']}; {'id': '285', 'type': 'attribute', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'set_yticklabels'}; {'id': '288', 'type': 'argument_list', 'children': ['289', '296', '299']}; {'id': '289', 'type': 'call', 'children': ['290', '295']}; {'id': '290', 'type': 'attribute', 'children': ['291', '294']}; {'id': '291', 'type': 'attribute', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'yaxis'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'get_majorticklabels'}; {'id': '295', 'type': 'argument_list', 'children': []}; {'id': '296', 'type': 'keyword_argument', 'children': ['297', '298']}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'rotation'}; {'id': '298', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '299', 'type': 'keyword_argument', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '302', 'type': 'expression_statement', 'children': ['303']}; {'id': '303', 'type': 'call', 'children': ['304', '309']}; {'id': '304', 'type': 'attribute', 'children': ['305', '308']}; {'id': '305', 'type': 'attribute', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'xaxis'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'set_ticks_position'}; {'id': '309', 'type': 'argument_list', 'children': ['310']}; {'id': '310', 'type': 'string', 'children': [], 'value': "'none'"}; {'id': '311', 'type': 'expression_statement', 'children': ['312']}; {'id': '312', 'type': 'call', 'children': ['313', '318']}; {'id': '313', 'type': 'attribute', 'children': ['314', '317']}; {'id': '314', 'type': 'attribute', 'children': ['315', '316']}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'yaxis'}; {'id': '317', 'type': 'identifier', 'children': [], 'value': 'set_ticks_position'}; {'id': '318', 'type': 'argument_list', 'children': ['319']}; {'id': '319', 'type': 'string', 'children': [], 'value': "'none'"}; {'id': '320', 'type': 'expression_statement', 'children': ['321']}; {'id': '321', 'type': 'call', 'children': ['322', '327']}; {'id': '322', 'type': 'attribute', 'children': ['323', '326']}; {'id': '323', 'type': 'attribute', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'patch'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '327', 'type': 'argument_list', 'children': ['328']}; {'id': '328', 'type': 'False', 'children': []}; {'id': '329', 'type': 'for_statement', 'children': ['330', '331', '334']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '331', 'type': 'attribute', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '333', 'type': 'identifier', 'children': [], 'value': 'texts'}; {'id': '334', 'type': 'block', 'children': ['335', '346']}; {'id': '335', 'type': 'expression_statement', 'children': ['336']}; {'id': '336', 'type': 'assignment', 'children': ['337', '338']}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '338', 'type': 'call', 'children': ['339', '340']}; {'id': '339', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '340', 'type': 'argument_list', 'children': ['341']}; {'id': '341', 'type': 'call', 'children': ['342', '345']}; {'id': '342', 'type': 'attribute', 'children': ['343', '344']}; {'id': '343', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'get_text'}; {'id': '345', 'type': 'argument_list', 'children': []}; {'id': '346', 'type': 'if_statement', 'children': ['347', '351', '359', '374', '386', '399', '413']}; {'id': '347', 'type': 'comparison_operator', 'children': ['348', '349', '350'], 'value': '<='}; {'id': '348', 'type': 'float', 'children': [], 'value': '0.95'}; {'id': '349', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '350', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '351', 'type': 'block', 'children': ['352']}; {'id': '352', 'type': 'expression_statement', 'children': ['353']}; {'id': '353', 'type': 'call', 'children': ['354', '357']}; {'id': '354', 'type': 'attribute', 'children': ['355', '356']}; {'id': '355', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'set_text'}; {'id': '357', 'type': 'argument_list', 'children': ['358']}; {'id': '358', 'type': 'string', 'children': [], 'value': "'<1'"}; {'id': '359', 'type': 'elif_clause', 'children': ['360', '366']}; {'id': '360', 'type': 'comparison_operator', 'children': ['361', '363', '364'], 'value': '<'}; {'id': '361', 'type': 'unary_operator', 'children': ['362'], 'value': '-'}; {'id': '362', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '363', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '364', 'type': 'unary_operator', 'children': ['365'], 'value': '-'}; {'id': '365', 'type': 'float', 'children': [], 'value': '0.95'}; {'id': '366', 'type': 'block', 'children': ['367']}; {'id': '367', 'type': 'expression_statement', 'children': ['368']}; {'id': '368', 'type': 'call', 'children': ['369', '372']}; {'id': '369', 'type': 'attribute', 'children': ['370', '371']}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '371', 'type': 'identifier', 'children': [], 'value': 'set_text'}; {'id': '372', 'type': 'argument_list', 'children': ['373']}; {'id': '373', 'type': 'string', 'children': [], 'value': "'>-1'"}; {'id': '374', 'type': 'elif_clause', 'children': ['375', '378']}; {'id': '375', 'type': 'comparison_operator', 'children': ['376', '377'], 'value': '=='}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '377', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '378', 'type': 'block', 'children': ['379']}; {'id': '379', 'type': 'expression_statement', 'children': ['380']}; {'id': '380', 'type': 'call', 'children': ['381', '384']}; {'id': '381', 'type': 'attribute', 'children': ['382', '383']}; {'id': '382', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '383', 'type': 'identifier', 'children': [], 'value': 'set_text'}; {'id': '384', 'type': 'argument_list', 'children': ['385']}; {'id': '385', 'type': 'string', 'children': [], 'value': "'1'"}; {'id': '386', 'type': 'elif_clause', 'children': ['387', '391']}; {'id': '387', 'type': 'comparison_operator', 'children': ['388', '389'], 'value': '=='}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '389', 'type': 'unary_operator', 'children': ['390'], 'value': '-'}; {'id': '390', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '391', 'type': 'block', 'children': ['392']}; {'id': '392', 'type': 'expression_statement', 'children': ['393']}; {'id': '393', 'type': 'call', 'children': ['394', '397']}; {'id': '394', 'type': 'attribute', 'children': ['395', '396']}; {'id': '395', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'set_text'}; {'id': '397', 'type': 'argument_list', 'children': ['398']}; {'id': '398', 'type': 'string', 'children': [], 'value': "'-1'"}; {'id': '399', 'type': 'elif_clause', 'children': ['400', '405']}; {'id': '400', 'type': 'comparison_operator', 'children': ['401', '403', '404'], 'value': '<'}; {'id': '401', 'type': 'unary_operator', 'children': ['402'], 'value': '-'}; {'id': '402', 'type': 'float', 'children': [], 'value': '0.05'}; {'id': '403', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '404', 'type': 'float', 'children': [], 'value': '0.05'}; {'id': '405', 'type': 'block', 'children': ['406']}; {'id': '406', 'type': 'expression_statement', 'children': ['407']}; {'id': '407', 'type': 'call', 'children': ['408', '411']}; {'id': '408', 'type': 'attribute', 'children': ['409', '410']}; {'id': '409', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '410', 'type': 'identifier', 'children': [], 'value': 'set_text'}; {'id': '411', 'type': 'argument_list', 'children': ['412']}; {'id': '412', 'type': 'string', 'children': [], 'value': "''"}; {'id': '413', 'type': 'else_clause', 'children': ['414']}; {'id': '414', 'type': 'block', 'children': ['415']}; {'id': '415', 'type': 'expression_statement', 'children': ['416']}; {'id': '416', 'type': 'call', 'children': ['417', '420']}; {'id': '417', 'type': 'attribute', 'children': ['418', '419']}; {'id': '418', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '419', 'type': 'identifier', 'children': [], 'value': 'set_text'}; {'id': '420', 'type': 'argument_list', 'children': ['421']}; {'id': '421', 'type': 'call', 'children': ['422', '423']}; {'id': '422', 'type': 'identifier', 'children': [], 'value': 'round'}; {'id': '423', 'type': 'argument_list', 'children': ['424', '425']}; {'id': '424', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '425', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '426', 'type': 'if_statement', 'children': ['427', '428', '435']}; {'id': '427', 'type': 'identifier', 'children': [], 'value': 'inline'}; {'id': '428', 'type': 'block', 'children': ['429']}; {'id': '429', 'type': 'expression_statement', 'children': ['430']}; {'id': '430', 'type': 'call', 'children': ['431', '434']}; {'id': '431', 'type': 'attribute', 'children': ['432', '433']}; {'id': '432', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '433', 'type': 'identifier', 'children': [], 'value': 'show'}; {'id': '434', 'type': 'argument_list', 'children': []}; {'id': '435', 'type': 'else_clause', 'children': ['436']}; {'id': '436', 'type': 'block', 'children': ['437']}; {'id': '437', 'type': 'return_statement', 'children': ['438']}; {'id': '438', 'type': 'identifier', 'children': [], 'value': 'ax0'} | def heatmap(df, inline=False,
filter=None, n=0, p=0, sort=None,
figsize=(20, 12), fontsize=16, labels=True,
cmap='RdBu', vmin=-1, vmax=1, cbar=True
):
df = nullity_filter(df, filter=filter, n=n, p=p)
df = nullity_sort(df, sort=sort)
plt.figure(figsize=figsize)
gs = gridspec.GridSpec(1, 1)
ax0 = plt.subplot(gs[0])
df = df.iloc[:,[i for i, n in enumerate(np.var(df.isnull(), axis='rows')) if n > 0]]
corr_mat = df.isnull().corr()
mask = np.zeros_like(corr_mat)
mask[np.triu_indices_from(mask)] = True
if labels:
sns.heatmap(corr_mat, mask=mask, cmap=cmap, ax=ax0, cbar=cbar,
annot=True, annot_kws={'size': fontsize - 2},
vmin=vmin, vmax=vmax)
else:
sns.heatmap(corr_mat, mask=mask, cmap=cmap, ax=ax0, cbar=cbar,
vmin=vmin, vmax=vmax)
ax0.xaxis.tick_bottom()
ax0.set_xticklabels(ax0.xaxis.get_majorticklabels(), rotation=45, ha='right', fontsize=fontsize)
ax0.set_yticklabels(ax0.yaxis.get_majorticklabels(), fontsize=fontsize, rotation=0)
ax0.set_yticklabels(ax0.yaxis.get_majorticklabels(), rotation=0, fontsize=fontsize)
ax0.xaxis.set_ticks_position('none')
ax0.yaxis.set_ticks_position('none')
ax0.patch.set_visible(False)
for text in ax0.texts:
t = float(text.get_text())
if 0.95 <= t < 1:
text.set_text('<1')
elif -1 < t <= -0.95:
text.set_text('>-1')
elif t == 1:
text.set_text('1')
elif t == -1:
text.set_text('-1')
elif -0.05 < t < 0.05:
text.set_text('')
else:
text.set_text(round(t, 1))
if inline:
plt.show()
else:
return ax0 |
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{'id': '153', 'type': 'identifier', 'children': [], 'value': 'astype'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'z'}; {'id': '160', 'type': 'call', 'children': ['161', '164']}; {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'hierarchy'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'linkage'}; {'id': '164', 'type': 'argument_list', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '167', 'type': 'if_statement', 'children': ['168', '170']}; {'id': '168', 'type': 'not_operator', 'children': ['169']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '170', 'type': 'block', 'children': ['171']}; {'id': '171', 'type': 'if_statement', 'children': ['172', '180', '185']}; {'id': '172', 'type': 'comparison_operator', 'children': ['173', '179'], 'value': '>'}; {'id': '173', 'type': 'call', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '175', 'type': 'argument_list', 'children': ['176']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '179', 'type': 'integer', 'children': [], 'value': '50'}; {'id': '180', 'type': 'block', 'children': ['181']}; {'id': '181', 'type': 'expression_statement', 'children': ['182']}; {'id': '182', 'type': 'assignment', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '184', 'type': 'string', 'children': [], 'value': "'left'"}; {'id': '185', 'type': 'else_clause', 'children': ['186']}; {'id': '186', 'type': 'block', 'children': ['187']}; {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'assignment', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '190', 'type': 'string', 'children': [], 'value': "'bottom'"}; {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'call', 'children': ['193', '196']}; {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'hierarchy'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'dendrogram'}; {'id': '196', 'type': 'argument_list', 'children': ['197', '198', '201', '210', '213', '219', '222']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'z'}; {'id': '198', 'type': 'keyword_argument', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '201', 'type': 'keyword_argument', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '203', 'type': 'call', 'children': ['204', '209']}; {'id': '204', 'type': 'attribute', 'children': ['205', '208']}; {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'tolist'}; {'id': '209', 'type': 'argument_list', 'children': []}; {'id': '210', 'type': 'keyword_argument', 'children': ['211', '212']}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'distance_sort'}; {'id': '212', 'type': 'string', 'children': [], 'value': "'descending'"}; {'id': '213', 'type': 'keyword_argument', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'link_color_func'}; {'id': '215', 'type': 'lambda', 'children': ['216', '218']}; {'id': '216', 'type': 'lambda_parameters', 'children': ['217']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '218', 'type': 'string', 'children': [], 'value': "'black'"}; {'id': '219', 'type': 'keyword_argument', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'leaf_font_size'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '222', 'type': 'keyword_argument', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '225', 'type': 'expression_statement', 'children': ['226']}; {'id': '226', 'type': 'call', 'children': ['227', '230']}; {'id': '227', 'type': 'attribute', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'set_aspect'}; {'id': '230', 'type': 'argument_list', 'children': ['231']}; {'id': '231', 'type': 'string', 'children': [], 'value': "'auto'"}; {'id': '232', 'type': 'expression_statement', 'children': ['233']}; {'id': '233', 'type': 'call', 'children': ['234', '237']}; {'id': '234', 'type': 'attribute', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'grid'}; {'id': '237', 'type': 'argument_list', 'children': ['238']}; {'id': '238', 'type': 'keyword_argument', 'children': ['239', '240']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '240', 'type': 'False', 'children': []}; {'id': '241', 'type': 'if_statement', 'children': ['242', '245']}; {'id': '242', 'type': 'comparison_operator', 'children': ['243', '244'], 'value': '=='}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '244', 'type': 'string', 'children': [], 'value': "'bottom'"}; {'id': '245', 'type': 'block', 'children': ['246']}; {'id': '246', 'type': 'expression_statement', 'children': ['247']}; {'id': '247', 'type': 'call', 'children': ['248', '253']}; {'id': '248', 'type': 'attribute', 'children': ['249', '252']}; {'id': '249', 'type': 'attribute', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'xaxis'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'tick_top'}; {'id': '253', 'type': 'argument_list', 'children': []}; {'id': '254', 'type': 'expression_statement', 'children': ['255']}; {'id': '255', 'type': 'call', 'children': ['256', '261']}; {'id': '256', 'type': 'attribute', 'children': ['257', '260']}; {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'xaxis'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'set_ticks_position'}; {'id': '261', 'type': 'argument_list', 'children': ['262']}; {'id': '262', 'type': 'string', 'children': [], 'value': "'none'"}; {'id': '263', 'type': 'expression_statement', 'children': ['264']}; {'id': '264', 'type': 'call', 'children': ['265', '270']}; {'id': '265', 'type': 'attribute', 'children': ['266', '269']}; {'id': '266', 'type': 'attribute', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'yaxis'}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'set_ticks_position'}; {'id': '270', 'type': 'argument_list', 'children': ['271']}; {'id': '271', 'type': 'string', 'children': [], 'value': "'none'"}; {'id': '272', 'type': 'expression_statement', 'children': ['273']}; {'id': '273', 'type': 'call', 'children': ['274', '281']}; {'id': '274', 'type': 'attribute', 'children': ['275', '280']}; {'id': '275', 'type': 'subscript', 'children': ['276', '279']}; {'id': '276', 'type': 'attribute', 'children': ['277', '278']}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'spines'}; {'id': '279', 'type': 'string', 'children': [], 'value': "'top'"}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '281', 'type': 'argument_list', 'children': ['282']}; {'id': '282', 'type': 'False', 'children': []}; {'id': '283', 'type': 'expression_statement', 'children': ['284']}; {'id': '284', 'type': 'call', 'children': ['285', '292']}; {'id': '285', 'type': 'attribute', 'children': ['286', '291']}; {'id': '286', 'type': 'subscript', 'children': ['287', '290']}; {'id': '287', 'type': 'attribute', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'spines'}; {'id': '290', 'type': 'string', 'children': [], 'value': "'right'"}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '292', 'type': 'argument_list', 'children': ['293']}; {'id': '293', 'type': 'False', 'children': []}; {'id': '294', 'type': 'expression_statement', 'children': ['295']}; {'id': '295', 'type': 'call', 'children': ['296', '303']}; {'id': '296', 'type': 'attribute', 'children': ['297', '302']}; {'id': '297', 'type': 'subscript', 'children': ['298', '301']}; {'id': '298', 'type': 'attribute', 'children': ['299', '300']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'spines'}; {'id': '301', 'type': 'string', 'children': [], 'value': "'bottom'"}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '303', 'type': 'argument_list', 'children': ['304']}; {'id': '304', 'type': 'False', 'children': []}; {'id': '305', 'type': 'expression_statement', 'children': ['306']}; {'id': '306', 'type': 'call', 'children': ['307', '314']}; {'id': '307', 'type': 'attribute', 'children': ['308', '313']}; {'id': '308', 'type': 'subscript', 'children': ['309', '312']}; {'id': '309', 'type': 'attribute', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '311', 'type': 'identifier', 'children': [], 'value': 'spines'}; {'id': '312', 'type': 'string', 'children': [], 'value': "'left'"}; {'id': '313', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '314', 'type': 'argument_list', 'children': ['315']}; {'id': '315', 'type': 'False', 'children': []}; {'id': '316', 'type': 'expression_statement', 'children': ['317']}; {'id': '317', 'type': 'call', 'children': ['318', '323']}; {'id': '318', 'type': 'attribute', 'children': ['319', '322']}; {'id': '319', 'type': 'attribute', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '321', 'type': 'identifier', 'children': [], 'value': 'patch'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'set_visible'}; {'id': '323', 'type': 'argument_list', 'children': ['324']}; {'id': '324', 'type': 'False', 'children': []}; {'id': '325', 'type': 'if_statement', 'children': ['326', '329', '349']}; {'id': '326', 'type': 'comparison_operator', 'children': ['327', '328'], 'value': '=='}; {'id': '327', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '328', 'type': 'string', 'children': [], 'value': "'bottom'"}; {'id': '329', 'type': 'block', 'children': ['330']}; {'id': '330', 'type': 'expression_statement', 'children': ['331']}; {'id': '331', 'type': 'call', 'children': ['332', '335']}; {'id': '332', 'type': 'attribute', 'children': ['333', '334']}; {'id': '333', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'set_xticklabels'}; {'id': '335', 'type': 'argument_list', 'children': ['336', '343', '346']}; {'id': '336', 'type': 'call', 'children': ['337', '342']}; {'id': '337', 'type': 'attribute', 'children': ['338', '341']}; {'id': '338', 'type': 'attribute', 'children': ['339', '340']}; {'id': '339', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'xaxis'}; {'id': '341', 'type': 'identifier', 'children': [], 'value': 'get_majorticklabels'}; {'id': '342', 'type': 'argument_list', 'children': []}; {'id': '343', 'type': 'keyword_argument', 'children': ['344', '345']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'rotation'}; {'id': '345', 'type': 'integer', 'children': [], 'value': '45'}; {'id': '346', 'type': 'keyword_argument', 'children': ['347', '348']}; {'id': '347', 'type': 'identifier', 'children': [], 'value': 'ha'}; {'id': '348', 'type': 'string', 'children': [], 'value': "'left'"}; {'id': '349', 'type': 'elif_clause', 'children': ['350', '353']}; {'id': '350', 'type': 'comparison_operator', 'children': ['351', '352'], 'value': '=='}; {'id': '351', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '352', 'type': 'string', 'children': [], 'value': "'top'"}; {'id': '353', 'type': 'block', 'children': ['354']}; {'id': '354', 'type': 'expression_statement', 'children': ['355']}; {'id': '355', 'type': 'call', 'children': ['356', '359']}; {'id': '356', 'type': 'attribute', 'children': ['357', '358']}; {'id': '357', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'set_xticklabels'}; {'id': '359', 'type': 'argument_list', 'children': ['360', '367', '370']}; {'id': '360', 'type': 'call', 'children': ['361', '366']}; {'id': '361', 'type': 'attribute', 'children': ['362', '365']}; {'id': '362', 'type': 'attribute', 'children': ['363', '364']}; {'id': '363', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'xaxis'}; {'id': '365', 'type': 'identifier', 'children': [], 'value': 'get_majorticklabels'}; {'id': '366', 'type': 'argument_list', 'children': []}; {'id': '367', 'type': 'keyword_argument', 'children': ['368', '369']}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'rotation'}; {'id': '369', 'type': 'integer', 'children': [], 'value': '45'}; {'id': '370', 'type': 'keyword_argument', 'children': ['371', '372']}; {'id': '371', 'type': 'identifier', 'children': [], 'value': 'ha'}; {'id': '372', 'type': 'string', 'children': [], 'value': "'right'"}; {'id': '373', 'type': 'if_statement', 'children': ['374', '381', '401']}; {'id': '374', 'type': 'boolean_operator', 'children': ['375', '378'], 'value': 'or'}; {'id': '375', 'type': 'comparison_operator', 'children': ['376', '377'], 'value': '=='}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '377', 'type': 'string', 'children': [], 'value': "'bottom'"}; {'id': '378', 'type': 'comparison_operator', 'children': ['379', '380'], 'value': '=='}; {'id': '379', 'type': 'identifier', 'children': [], 'value': 'orientation'}; {'id': '380', 'type': 'string', 'children': [], 'value': "'top'"}; {'id': '381', 'type': 'block', 'children': ['382']}; {'id': '382', 'type': 'expression_statement', 'children': ['383']}; {'id': '383', 'type': 'call', 'children': ['384', '387']}; {'id': '384', 'type': 'attribute', 'children': ['385', '386']}; {'id': '385', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'tick_params'}; {'id': '387', 'type': 'argument_list', 'children': ['388', '391']}; {'id': '388', 'type': 'keyword_argument', 'children': ['389', '390']}; {'id': '389', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '390', 'type': 'string', 'children': [], 'value': "'y'"}; {'id': '391', 'type': 'keyword_argument', 'children': ['392', '393']}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'labelsize'}; {'id': '393', 'type': 'call', 'children': ['394', '395']}; {'id': '394', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '395', 'type': 'argument_list', 'children': ['396']}; {'id': '396', 'type': 'binary_operator', 'children': ['397', '400'], 'value': '*'}; {'id': '397', 'type': 'binary_operator', 'children': ['398', '399'], 'value': '/'}; {'id': '398', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '399', 'type': 'integer', 'children': [], 'value': '16'}; {'id': '400', 'type': 'integer', 'children': [], 'value': '20'}; {'id': '401', 'type': 'else_clause', 'children': ['402']}; {'id': '402', 'type': 'block', 'children': ['403']}; {'id': '403', 'type': 'expression_statement', 'children': ['404']}; {'id': '404', 'type': 'call', 'children': ['405', '408']}; {'id': '405', 'type': 'attribute', 'children': ['406', '407']}; {'id': '406', 'type': 'identifier', 'children': [], 'value': 'ax0'}; {'id': '407', 'type': 'identifier', 'children': [], 'value': 'tick_params'}; {'id': '408', 'type': 'argument_list', 'children': ['409', '412']}; {'id': '409', 'type': 'keyword_argument', 'children': ['410', '411']}; {'id': '410', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '411', 'type': 'string', 'children': [], 'value': "'x'"}; {'id': '412', 'type': 'keyword_argument', 'children': ['413', '414']}; {'id': '413', 'type': 'identifier', 'children': [], 'value': 'labelsize'}; {'id': '414', 'type': 'call', 'children': ['415', '416']}; {'id': '415', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '416', 'type': 'argument_list', 'children': ['417']}; {'id': '417', 'type': 'binary_operator', 'children': ['418', '421'], 'value': '*'}; {'id': '418', 'type': 'binary_operator', 'children': ['419', '420'], 'value': '/'}; {'id': '419', 'type': 'identifier', 'children': [], 'value': 'fontsize'}; {'id': '420', 'type': 'integer', 'children': [], 'value': '16'}; {'id': '421', 'type': 'integer', 'children': [], 'value': '20'}; {'id': '422', 'type': 'if_statement', 'children': ['423', '424', '431']}; {'id': '423', 'type': 'identifier', 'children': [], 'value': 'inline'}; {'id': '424', 'type': 'block', 'children': ['425']}; {'id': '425', 'type': 'expression_statement', 'children': ['426']}; {'id': '426', 'type': 'call', 'children': ['427', '430']}; {'id': '427', 'type': 'attribute', 'children': ['428', '429']}; {'id': '428', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '429', 'type': 'identifier', 'children': [], 'value': 'show'}; {'id': '430', 'type': 'argument_list', 'children': []}; {'id': '431', 'type': 'else_clause', 'children': ['432']}; {'id': '432', 'type': 'block', 'children': ['433']}; {'id': '433', 'type': 'return_statement', 'children': ['434']}; {'id': '434', 'type': 'identifier', 'children': [], 'value': 'ax0'} | def dendrogram(df, method='average',
filter=None, n=0, p=0, sort=None,
orientation=None, figsize=None,
fontsize=16, inline=False
):
if not figsize:
if len(df.columns) <= 50 or orientation == 'top' or orientation == 'bottom':
figsize = (25, 10)
else:
figsize = (25, (25 + len(df.columns) - 50)*0.5)
plt.figure(figsize=figsize)
gs = gridspec.GridSpec(1, 1)
ax0 = plt.subplot(gs[0])
df = nullity_filter(df, filter=filter, n=n, p=p)
df = nullity_sort(df, sort=sort)
x = np.transpose(df.isnull().astype(int).values)
z = hierarchy.linkage(x, method)
if not orientation:
if len(df.columns) > 50:
orientation = 'left'
else:
orientation = 'bottom'
hierarchy.dendrogram(z,
orientation=orientation,
labels=df.columns.tolist(),
distance_sort='descending',
link_color_func=lambda c: 'black',
leaf_font_size=fontsize,
ax=ax0
)
ax0.set_aspect('auto')
ax0.grid(b=False)
if orientation == 'bottom':
ax0.xaxis.tick_top()
ax0.xaxis.set_ticks_position('none')
ax0.yaxis.set_ticks_position('none')
ax0.spines['top'].set_visible(False)
ax0.spines['right'].set_visible(False)
ax0.spines['bottom'].set_visible(False)
ax0.spines['left'].set_visible(False)
ax0.patch.set_visible(False)
if orientation == 'bottom':
ax0.set_xticklabels(ax0.xaxis.get_majorticklabels(), rotation=45, ha='left')
elif orientation == 'top':
ax0.set_xticklabels(ax0.xaxis.get_majorticklabels(), rotation=45, ha='right')
if orientation == 'bottom' or orientation == 'top':
ax0.tick_params(axis='y', labelsize=int(fontsize / 16 * 20))
else:
ax0.tick_params(axis='x', labelsize=int(fontsize / 16 * 20))
if inline:
plt.show()
else:
return ax0 |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'nullity_sort'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9']}; {'id': '9', 'type': 'if_statement', 'children': ['10', '13', '36', '68']}; {'id': '10', 'type': 'comparison_operator', 'children': ['11', '12'], 'value': '=='}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '12', 'type': 'string', 'children': [], 'value': "'ascending'"}; {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'return_statement', 'children': ['15']}; {'id': '15', 'type': 'subscript', 'children': ['16', '19', '34']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'iloc'}; {'id': '19', 'type': 'call', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'argsort'}; {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'attribute', 'children': ['25', '33']}; {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '29', 'type': 'argument_list', 'children': ['30']}; {'id': '30', 'type': 'keyword_argument', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '32', 'type': 'string', 'children': [], 'value': "'columns'"}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '34', 'type': 'slice', 'children': ['35']}; {'id': '35', 'type': 'colon', 'children': []}; {'id': '36', 'type': 'elif_clause', 'children': ['37', '40']}; {'id': '37', 'type': 'comparison_operator', 'children': ['38', '39'], 'value': '=='}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '39', 'type': 'string', 'children': [], 'value': "'descending'"}; {'id': '40', 'type': 'block', 'children': ['41']}; {'id': '41', 'type': 'return_statement', 'children': ['42']}; {'id': '42', 'type': 'subscript', 'children': ['43', '46', '66']}; {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'iloc'}; {'id': '46', 'type': 'call', 'children': ['47', '50']}; {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'flipud'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}; {'id': '51', 'type': 'call', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'argsort'}; {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'attribute', 'children': ['57', '65']}; {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'keyword_argument', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '64', 'type': 'string', 'children': [], 'value': "'columns'"}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '66', 'type': 'slice', 'children': ['67']}; {'id': '67', 'type': 'colon', 'children': []}; {'id': '68', 'type': 'else_clause', 'children': ['69']}; {'id': '69', 'type': 'block', 'children': ['70']}; {'id': '70', 'type': 'return_statement', 'children': ['71']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'df'} | def nullity_sort(df, sort=None):
if sort == 'ascending':
return df.iloc[np.argsort(df.count(axis='columns').values), :]
elif sort == 'descending':
return df.iloc[np.flipud(np.argsort(df.count(axis='columns').values)), :]
else:
return df |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sortino_ratio'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'required_return'}; {'id': '7', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'period'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'DAILY'}; {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'annualization'}; {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '16', 'type': 'None', 'children': []}; {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': '_downside_risk'}; {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'block', 'children': ['21', '27', '45', '53', '82', '95', '103', '115', '131', '142', '171']}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'allocated_output'}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '26'], 'value': 'is'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '26', 'type': 'None', 'children': []}; {'id': '27', 'type': 'if_statement', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'allocated_output'}; {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'empty'}; {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'subscript', 'children': ['39', '42']}; {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '42', 'type': 'slice', 'children': ['43', '44']}; {'id': '43', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '44', 'type': 'colon', 'children': []}; {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'return_1d'}; {'id': '48', 'type': 'comparison_operator', 'children': ['49', '52'], 'value': '=='}; {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'ndim'}; {'id': '52', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '53', 'type': 'if_statement', 'children': ['54', '60']}; {'id': '54', 'type': 'comparison_operator', 'children': ['55', '59'], 'value': '<'}; {'id': '55', 'type': 'call', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '57', 'type': 'argument_list', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '59', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '60', 'type': 'block', 'children': ['61', '69', '80']}; {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '66']}; {'id': '63', 'type': 'subscript', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '65', 'type': 'tuple', 'children': []}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'nan'}; {'id': '69', 'type': 'if_statement', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'return_1d'}; {'id': '71', 'type': 'block', 'children': ['72']}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}; {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '79', 'type': 'argument_list', 'children': []}; {'id': '80', 'type': 'return_statement', 'children': ['81']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}; {'id': '83', 'type': 'assignment', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'adj_returns'}; {'id': '85', 'type': 'call', 'children': ['86', '89']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'asanyarray'}; {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'call', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': '_adjust_returns'}; {'id': '92', 'type': 'argument_list', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'required_return'}; {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'assignment', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'ann_factor'}; {'id': '98', 'type': 'call', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'annualization_factor'}; {'id': '100', 'type': 'argument_list', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'period'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'annualization'}; {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'average_annual_return'}; {'id': '106', 'type': 'binary_operator', 'children': ['107', '114'], 'value': '*'}; {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'nanmean'}; {'id': '109', 'type': 'argument_list', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'adj_returns'}; {'id': '111', 'type': 'keyword_argument', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '113', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'ann_factor'}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'annualized_downside_risk'}; {'id': '118', 'type': '()', 'children': ['119']}; {'id': '119', 'type': 'conditional_expression', 'children': ['120', '121', '124'], 'value': 'if'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': '_downside_risk'}; {'id': '121', 'type': 'comparison_operator', 'children': ['122', '123'], 'value': 'is'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': '_downside_risk'}; {'id': '123', 'type': 'None', 'children': []}; {'id': '124', 'type': 'call', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'downside_risk'}; {'id': '126', 'type': 'argument_list', 'children': ['127', '128', '129', '130']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'required_return'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'period'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'annualization'}; {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'call', 'children': ['133', '136']}; {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'divide'}; {'id': '136', 'type': 'argument_list', 'children': ['137', '138', '139']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'average_annual_return'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'annualized_downside_risk'}; {'id': '139', 'type': 'keyword_argument', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '142', 'type': 'if_statement', 'children': ['143', '144', '153']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'return_1d'}; {'id': '144', 'type': 'block', 'children': ['145']}; {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}; {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '152', 'type': 'argument_list', 'children': []}; {'id': '153', 'type': 'elif_clause', 'children': ['154', '161']}; {'id': '154', 'type': 'call', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'DataFrame'}; {'id': '161', 'type': 'block', 'children': ['162']}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}; {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'Series'}; {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '171', 'type': 'return_statement', 'children': ['172']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'out'} | def sortino_ratio(returns,
required_return=0,
period=DAILY,
annualization=None,
out=None,
_downside_risk=None):
allocated_output = out is None
if allocated_output:
out = np.empty(returns.shape[1:])
return_1d = returns.ndim == 1
if len(returns) < 2:
out[()] = np.nan
if return_1d:
out = out.item()
return out
adj_returns = np.asanyarray(_adjust_returns(returns, required_return))
ann_factor = annualization_factor(period, annualization)
average_annual_return = nanmean(adj_returns, axis=0) * ann_factor
annualized_downside_risk = (
_downside_risk
if _downside_risk is not None else
downside_risk(returns, required_return, period, annualization)
)
np.divide(average_annual_return, annualized_downside_risk, out=out)
if return_1d:
out = out.item()
elif isinstance(returns, pd.DataFrame):
out = pd.Series(out)
return out |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'downside_risk'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'required_return'}; {'id': '7', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'period'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'DAILY'}; {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'annualization'}; {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '16', 'type': 'None', 'children': []}; {'id': '17', 'type': 'block', 'children': ['18', '24', '42', '50', '79', '87', '114', '124', '135', '145', '161', '195']}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}; {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'allocated_output'}; {'id': '21', 'type': 'comparison_operator', 'children': ['22', '23'], 'value': 'is'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'if_statement', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'allocated_output'}; {'id': '26', 'type': 'block', 'children': ['27']}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '30', 'type': 'call', 'children': ['31', '34']}; {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'empty'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}; {'id': '35', 'type': 'subscript', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '39', 'type': 'slice', 'children': ['40', '41']}; {'id': '40', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '41', 'type': 'colon', 'children': []}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'returns_1d'}; {'id': '45', 'type': 'comparison_operator', 'children': ['46', '49'], 'value': '=='}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'ndim'}; {'id': '49', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '50', 'type': 'if_statement', 'children': ['51', '57']}; {'id': '51', 'type': 'comparison_operator', 'children': ['52', '56'], 'value': '<'}; {'id': '52', 'type': 'call', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '56', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '57', 'type': 'block', 'children': ['58', '66', '77']}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}; {'id': '59', 'type': 'assignment', 'children': ['60', '63']}; {'id': '60', 'type': 'subscript', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '62', 'type': 'tuple', 'children': []}; {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'nan'}; {'id': '66', 'type': 'if_statement', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'returns_1d'}; {'id': '68', 'type': 'block', 'children': ['69']}; {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '72', 'type': 'call', 'children': ['73', '76']}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '76', 'type': 'argument_list', 'children': []}; {'id': '77', 'type': 'return_statement', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'ann_factor'}; {'id': '82', 'type': 'call', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'annualization_factor'}; {'id': '84', 'type': 'argument_list', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'period'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'annualization'}; {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'downside_diff'}; {'id': '90', 'type': 'call', 'children': ['91', '94']}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'clip'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '110', '113']}; {'id': '95', 'type': 'call', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': '_adjust_returns'}; {'id': '97', 'type': 'argument_list', 'children': ['98', '104']}; {'id': '98', 'type': 'call', 'children': ['99', '102']}; {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'asanyarray'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '104', 'type': 'call', 'children': ['105', '108']}; {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'asanyarray'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'required_return'}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'NINF'}; {'id': '113', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}; {'id': '115', 'type': 'call', 'children': ['116', '119']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'square'}; {'id': '119', 'type': 'argument_list', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'downside_diff'}; {'id': '121', 'type': 'keyword_argument', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'downside_diff'}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}; {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'nanmean'}; {'id': '127', 'type': 'argument_list', 'children': ['128', '129', '132']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'downside_diff'}; {'id': '129', 'type': 'keyword_argument', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '131', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '132', 'type': 'keyword_argument', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '135', 'type': 'expression_statement', 'children': ['136']}; {'id': '136', 'type': 'call', 'children': ['137', '140']}; {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'sqrt'}; {'id': '140', 'type': 'argument_list', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '142', 'type': 'keyword_argument', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'call', 'children': ['147', '150']}; {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'multiply'}; {'id': '150', 'type': 'argument_list', 'children': ['151', '152', '158']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '152', 'type': 'call', 'children': ['153', '156']}; {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'sqrt'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'ann_factor'}; {'id': '158', 'type': 'keyword_argument', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '161', 'type': 'if_statement', 'children': ['162', '163', '172']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'returns_1d'}; {'id': '163', 'type': 'block', 'children': ['164']}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}; {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '171', 'type': 'argument_list', 'children': []}; {'id': '172', 'type': 'elif_clause', 'children': ['173', '180']}; {'id': '173', 'type': 'call', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '175', 'type': 'argument_list', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'DataFrame'}; {'id': '180', 'type': 'block', 'children': ['181']}; {'id': '181', 'type': 'expression_statement', 'children': ['182']}; {'id': '182', 'type': 'assignment', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '184', 'type': 'call', 'children': ['185', '188']}; {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'Series'}; {'id': '188', 'type': 'argument_list', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '190', 'type': 'keyword_argument', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '192', 'type': 'attribute', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'returns'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '195', 'type': 'return_statement', 'children': ['196']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'out'} | def downside_risk(returns,
required_return=0,
period=DAILY,
annualization=None,
out=None):
allocated_output = out is None
if allocated_output:
out = np.empty(returns.shape[1:])
returns_1d = returns.ndim == 1
if len(returns) < 1:
out[()] = np.nan
if returns_1d:
out = out.item()
return out
ann_factor = annualization_factor(period, annualization)
downside_diff = np.clip(
_adjust_returns(
np.asanyarray(returns),
np.asanyarray(required_return),
),
np.NINF,
0,
)
np.square(downside_diff, out=downside_diff)
nanmean(downside_diff, axis=0, out=out)
np.sqrt(out, out=out)
np.multiply(out, np.sqrt(ann_factor), out=out)
if returns_1d:
out = out.item()
elif isinstance(returns, pd.DataFrame):
out = pd.Series(out, index=returns.columns)
return out |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'GetLoadingOrder'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'block', 'children': ['6', '10', '39']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '9', 'type': 'dictionary', 'children': []}; {'id': '10', 'type': 'for_statement', 'children': ['11', '14', '21']}; {'id': '11', 'type': 'pattern_list', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'mapping'}; {'id': '14', 'type': 'call', 'children': ['15', '20']}; {'id': '15', 'type': 'attribute', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': '_file_mapping'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'iteritems'}; {'id': '20', 'type': 'argument_list', 'children': []}; {'id': '21', 'type': 'block', 'children': ['22', '28']}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'loading_order'}; {'id': '25', 'type': 'subscript', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'mapping'}; {'id': '27', 'type': 'string', 'children': [], 'value': "'loading_order'"}; {'id': '28', 'type': 'if_statement', 'children': ['29', '32']}; {'id': '29', 'type': 'comparison_operator', 'children': ['30', '31'], 'value': 'is'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'loading_order'}; {'id': '31', 'type': 'None', 'children': []}; {'id': '32', 'type': 'block', 'children': ['33']}; {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '38']}; {'id': '35', 'type': 'subscript', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'loading_order'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '39', 'type': 'return_statement', 'children': ['40']}; {'id': '40', 'type': 'call', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '42', 'type': 'generator_expression', 'children': ['43', '46']}; {'id': '43', 'type': 'subscript', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '46', 'type': 'for_in_clause', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '48', 'type': 'call', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'result'} | def GetLoadingOrder(self):
result = {}
for filename, mapping in self._file_mapping.iteritems():
loading_order = mapping['loading_order']
if loading_order is not None:
result[loading_order] = filename
return list(result[key] for key in sorted(result)) |
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context_attributes = ['_type']
context_attributes.extend(ExceptionWithContext.CONTEXT_PARTS)
context_attributes.extend(self._GetExtraOrderAttributes())
tokens = []
for context_attribute in context_attributes:
tokens.append(getattr(self, context_attribute, None))
return tokens |
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{'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '18', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '19', 'type': 'comparison_operator', 'children': ['20', '23'], 'value': '>='}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'shape_pt_sequence'}; {'id': '23', 'type': 'subscript', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '27', 'type': 'unary_operator', 'children': ['28'], 'value': '-'}; {'id': '28', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '39', 'type': 'elif_clause', 'children': ['40', '49']}; {'id': '40', 'type': 'comparison_operator', 'children': ['41', '44'], 'value': '<='}; {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'shape_pt_sequence'}; {'id': '44', 'type': 'subscript', 'children': ['45', '48']}; {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '48', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '49', 'type': 'block', 'children': ['50']}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}; {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '53', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '54', 'type': 'else_clause', 'children': ['55']}; {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}; {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'bisect'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'bisect'}; {'id': '63', 'type': 'argument_list', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'shape_pt_sequence'}; {'id': '70', 'type': 'if_statement', 'children': ['71', '78']}; {'id': '71', 'type': 'comparison_operator', 'children': ['72', '75'], 'value': 'in'}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'shape_pt_sequence'}; {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '78', 'type': 'block', 'children': ['79']}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '84']}; {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'problems'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'InvalidValue'}; {'id': '84', 'type': 'argument_list', 'children': ['85', '86', '89']}; {'id': '85', 'type': 'string', 'children': [], 'value': "'shape_pt_sequence'"}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'shape_pt_sequence'}; {'id': '89', 'type': 'binary_operator', 'children': ['90', '93'], 'value': '%'}; {'id': '90', 'type': 'concatenated_string', 'children': ['91', '92']}; {'id': '91', 'type': 'string', 'children': [], 'value': "'The sequence number %d occurs more than once in '"}; {'id': '92', 'type': 'string', 'children': [], 'value': "'shape %s.'"}; {'id': '93', 'type': 'tuple', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'shape_pt_sequence'}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'shape_id'}; {'id': '100', 'type': 'if_statement', 'children': ['101', '115']}; {'id': '101', 'type': 'boolean_operator', 'children': ['102', '107'], 'value': 'and'}; {'id': '102', 'type': 'comparison_operator', 'children': ['103', '106'], 'value': 'is'}; {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'}; {'id': '106', 'type': 'None', 'children': []}; {'id': '107', 'type': 'comparison_operator', 'children': ['108', '114'], 'value': '>'}; {'id': '108', 'type': 'call', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '114', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '115', 'type': 'block', 'children': ['116', '158']}; {'id': '116', 'type': 'if_statement', 'children': ['117', '136']}; {'id': '117', 'type': '()', 'children': ['118']}; {'id': '118', 'type': 'boolean_operator', 'children': ['119', '127'], 'value': 'and'}; {'id': '119', 'type': 'comparison_operator', 'children': ['120', '121'], 'value': '!='}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '121', 'type': 'call', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '123', 'type': 'argument_list', 'children': ['124']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '127', 'type': 'comparison_operator', 'children': ['128', '131'], 'value': '>'}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'}; {'id': '131', 'type': 'subscript', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'distance'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '136', 'type': 'block', 'children': ['137']}; {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'call', 'children': ['139', '142']}; {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'problems'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'InvalidValue'}; {'id': '142', 'type': 'argument_list', 'children': ['143', '144', '147']}; {'id': '143', 'type': 'string', 'children': [], 'value': "'shape_dist_traveled'"}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'}; {'id': '147', 'type': 'binary_operator', 'children': ['148', '153'], 'value': '%'}; {'id': '148', 'type': 'concatenated_string', 'children': ['149', '150', '151', '152']}; {'id': '149', 'type': 'string', 'children': [], 'value': "'Each subsequent point in a shape should have '"}; {'id': '150', 'type': 'string', 'children': [], 'value': "'a distance value that shouldn\\'t be larger '"}; {'id': '151', 'type': 'string', 'children': [], 'value': "'than the next ones. In this case, the next '"}; {'id': '152', 'type': 'string', 'children': [], 'value': "'distance was %f.'"}; {'id': '153', 'type': 'subscript', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'distance'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '158', 'type': 'if_statement', 'children': ['159', '175']}; {'id': '159', 'type': '()', 'children': ['160']}; {'id': '160', 'type': 'boolean_operator', 'children': ['161', '164'], 'value': 'and'}; {'id': '161', 'type': 'comparison_operator', 'children': ['162', '163'], 'value': '>'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '163', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '164', 'type': 'comparison_operator', 'children': ['165', '168'], 'value': '<'}; {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'}; {'id': '168', 'type': 'subscript', 'children': ['169', '172']}; {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'distance'}; {'id': '172', 'type': 'binary_operator', 'children': ['173', '174'], 'value': '-'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '174', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '175', 'type': 'block', 'children': ['176']}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}; {'id': '177', 'type': 'call', 'children': ['178', '181']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'problems'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'InvalidValue'}; {'id': '181', 'type': 'argument_list', 'children': ['182', '183', '186']}; {'id': '182', 'type': 'string', 'children': [], 'value': "'shape_dist_traveled'"}; {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'}; {'id': '186', 'type': 'binary_operator', 'children': ['187', '192'], 'value': '%'}; {'id': '187', 'type': 'concatenated_string', 'children': ['188', '189', '190', '191']}; {'id': '188', 'type': 'string', 'children': [], 'value': "'Each subsequent point in a shape should have '"}; {'id': '189', 'type': 'string', 'children': [], 'value': "'a distance value that\\'s at least as large as '"}; {'id': '190', 'type': 'string', 'children': [], 'value': "'the previous ones. In this case, the previous '"}; {'id': '191', 'type': 'string', 'children': [], 'value': "'distance was %f.'"}; {'id': '192', 'type': 'subscript', 'children': ['193', '196']}; {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'distance'}; {'id': '196', 'type': 'binary_operator', 'children': ['197', '198'], 'value': '-'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '198', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '199', 'type': 'if_statement', 'children': ['200', '207']}; {'id': '200', 'type': 'comparison_operator', 'children': ['201', '204'], 'value': '>'}; {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'max_distance'}; {'id': '207', 'type': 'block', 'children': ['208']}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}; {'id': '209', 'type': 'assignment', 'children': ['210', '213']}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'max_distance'}; {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}; {'id': '217', 'type': 'call', 'children': ['218', '223']}; {'id': '218', 'type': 'attribute', 'children': ['219', '222']}; {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'sequence'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'insert'}; {'id': '223', 'type': 'argument_list', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'shape_pt_sequence'}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}; {'id': '229', 'type': 'call', 'children': ['230', '235']}; {'id': '230', 'type': 'attribute', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'distance'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'insert'}; {'id': '235', 'type': 'argument_list', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'}; {'id': '240', 'type': 'expression_statement', 'children': ['241']}; {'id': '241', 'type': 'call', 'children': ['242', '247']}; {'id': '242', 'type': 'attribute', 'children': ['243', '246']}; {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'points'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'insert'}; {'id': '247', 'type': 'argument_list', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '249', 'type': 'tuple', 'children': ['250', '253', '256']}; {'id': '250', 'type': 'attribute', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'shape_pt_lat'}; {'id': '253', 'type': 'attribute', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'shape_pt_lon'}; {'id': '256', 'type': 'attribute', 'children': ['257', '258']}; {'id': '257', 'type': 'identifier', 'children': [], 'value': 'shapepoint'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'} | def AddShapePointObjectUnsorted(self, shapepoint, problems):
if (len(self.sequence) == 0 or
shapepoint.shape_pt_sequence >= self.sequence[-1]):
index = len(self.sequence)
elif shapepoint.shape_pt_sequence <= self.sequence[0]:
index = 0
else:
index = bisect.bisect(self.sequence, shapepoint.shape_pt_sequence)
if shapepoint.shape_pt_sequence in self.sequence:
problems.InvalidValue('shape_pt_sequence', shapepoint.shape_pt_sequence,
'The sequence number %d occurs more than once in '
'shape %s.' %
(shapepoint.shape_pt_sequence, self.shape_id))
if shapepoint.shape_dist_traveled is not None and len(self.sequence) > 0:
if (index != len(self.sequence) and
shapepoint.shape_dist_traveled > self.distance[index]):
problems.InvalidValue('shape_dist_traveled',
shapepoint.shape_dist_traveled,
'Each subsequent point in a shape should have '
'a distance value that shouldn\'t be larger '
'than the next ones. In this case, the next '
'distance was %f.' % self.distance[index])
if (index > 0 and
shapepoint.shape_dist_traveled < self.distance[index - 1]):
problems.InvalidValue('shape_dist_traveled',
shapepoint.shape_dist_traveled,
'Each subsequent point in a shape should have '
'a distance value that\'s at least as large as '
'the previous ones. In this case, the previous '
'distance was %f.' % self.distance[index - 1])
if shapepoint.shape_dist_traveled > self.max_distance:
self.max_distance = shapepoint.shape_dist_traveled
self.sequence.insert(index, shapepoint.shape_pt_sequence)
self.distance.insert(index, shapepoint.shape_dist_traveled)
self.points.insert(index, (shapepoint.shape_pt_lat,
shapepoint.shape_pt_lon,
shapepoint.shape_dist_traveled)) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'GetStopTimes'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'problems'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '21', '37', '41', '51', '62', '138']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'cursor'}; {'id': '12', 'type': 'call', 'children': ['13', '20']}; {'id': '13', 'type': 'attribute', 'children': ['14', '19']}; {'id': '14', 'type': 'attribute', 'children': ['15', '18']}; {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': '_schedule'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': '_connection'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'cursor'}; {'id': '20', 'type': 'argument_list', 'children': []}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'call', 'children': ['23', '26']}; {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'cursor'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'execute'}; {'id': '26', 'type': 'argument_list', 'children': ['27', '33']}; {'id': '27', 'type': 'concatenated_string', 'children': ['28', '29', '30', '31', '32']}; {'id': '28', 'type': 'string', 'children': [], 'value': "'SELECT arrival_secs,departure_secs,stop_headsign,pickup_type,'"}; {'id': '29', 'type': 'string', 'children': [], 'value': "'drop_off_type,shape_dist_traveled,stop_id,stop_sequence,timepoint '"}; {'id': '30', 'type': 'string', 'children': [], 'value': "'FROM stop_times '"}; {'id': '31', 'type': 'string', 'children': [], 'value': "'WHERE trip_id=? '"}; {'id': '32', 'type': 'string', 'children': [], 'value': "'ORDER BY stop_sequence'"}; {'id': '33', 'type': 'tuple', 'children': ['34']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'trip_id'}; {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'stop_times'}; {'id': '40', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'stoptime_class'}; {'id': '44', 'type': 'attribute', 'children': ['45', '50']}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'GetGtfsFactory'}; {'id': '49', 'type': 'argument_list', 'children': []}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'StopTime'}; {'id': '51', 'type': 'if_statement', 'children': ['52', '55']}; {'id': '52', 'type': 'comparison_operator', 'children': ['53', '54'], 'value': 'is'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'problems'}; {'id': '54', 'type': 'None', 'children': []}; {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}; {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'problems'}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'problems_module'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'default_problem_reporter'}; {'id': '62', 'type': 'for_statement', 'children': ['63', '64', '69']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '64', 'type': 'call', 'children': ['65', '68']}; {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'cursor'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'fetchall'}; {'id': '68', 'type': 'argument_list', 'children': []}; {'id': '69', 'type': 'block', 'children': ['70', '83']}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}; {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '73', 'type': 'call', 'children': ['74', '79']}; {'id': '74', 'type': 'attribute', 'children': ['75', '78']}; {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': '_schedule'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'GetStop'}; {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'subscript', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '82', 'type': 'integer', 'children': [], 'value': '6'}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}; {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'stop_times'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}; {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'stoptime_class'}; {'id': '91', 'type': 'argument_list', 'children': ['92', '95', '98', '103', '108', '113', '118', '123', '128', '133']}; {'id': '92', 'type': 'keyword_argument', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'problems'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'problems'}; {'id': '95', 'type': 'keyword_argument', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '98', 'type': 'keyword_argument', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'arrival_secs'}; {'id': '100', 'type': 'subscript', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '102', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '103', 'type': 'keyword_argument', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'departure_secs'}; {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '107', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '108', 'type': 'keyword_argument', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'stop_headsign'}; {'id': '110', 'type': 'subscript', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '112', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '113', 'type': 'keyword_argument', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'pickup_type'}; {'id': '115', 'type': 'subscript', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '117', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '118', 'type': 'keyword_argument', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'drop_off_type'}; {'id': '120', 'type': 'subscript', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '123', 'type': 'keyword_argument', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'shape_dist_traveled'}; {'id': '125', 'type': 'subscript', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '127', 'type': 'integer', 'children': [], 'value': '5'}; {'id': '128', 'type': 'keyword_argument', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'stop_sequence'}; {'id': '130', 'type': 'subscript', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '132', 'type': 'integer', 'children': [], 'value': '7'}; {'id': '133', 'type': 'keyword_argument', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'timepoint'}; {'id': '135', 'type': 'subscript', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '137', 'type': 'integer', 'children': [], 'value': '8'}; {'id': '138', 'type': 'return_statement', 'children': ['139']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'stop_times'} | def GetStopTimes(self, problems=None):
cursor = self._schedule._connection.cursor()
cursor.execute(
'SELECT arrival_secs,departure_secs,stop_headsign,pickup_type,'
'drop_off_type,shape_dist_traveled,stop_id,stop_sequence,timepoint '
'FROM stop_times '
'WHERE trip_id=? '
'ORDER BY stop_sequence', (self.trip_id,))
stop_times = []
stoptime_class = self.GetGtfsFactory().StopTime
if problems is None:
problems = problems_module.default_problem_reporter
for row in cursor.fetchall():
stop = self._schedule.GetStop(row[6])
stop_times.append(stoptime_class(problems=problems,
stop=stop,
arrival_secs=row[0],
departure_secs=row[1],
stop_headsign=row[2],
pickup_type=row[3],
drop_off_type=row[4],
shape_dist_traveled=row[5],
stop_sequence=row[7],
timepoint=row[8]))
return stop_times |
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start_times = []
for freq_tuple in self.GetFrequencyTuples():
(start_secs, end_secs, headway_secs) = freq_tuple[0:3]
run_secs = start_secs
while run_secs < end_secs:
start_times.append(run_secs)
run_secs += headway_secs
return start_times |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'create'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '6', 'type': 'block', 'children': ['7', '12', '50', '63', '74', '90', '103', '112', '146', '162', '191', '228', '234', '280', '301', '338', '381']}; {'id': '7', 'type': 'import_from_statement', 'children': ['8', '10']}; {'id': '8', 'type': 'relative_import', 'children': ['9']}; {'id': '9', 'type': 'import_prefix', 'children': []}; {'id': '10', 'type': 'dotted_name', 'children': ['11']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': '_segyio'}; {'id': '12', 'type': 'if_statement', 'children': ['13', '18', '25']}; {'id': '13', 'type': 'not_operator', 'children': ['14']}; {'id': '14', 'type': 'call', 'children': ['15', '16']}; 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{'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'offsets'}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}; {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'ext_headers'}; {'id': '53', 'type': 'conditional_expression', 'children': ['54', '57', '62'], 'value': 'if'}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'ext_headers'}; {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'hasattr'}; {'id': '59', 'type': 'argument_list', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '61', 'type': 'string', 'children': [], 'value': "'ext_headers'"}; 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{'id': '140', 'type': 'attribute', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'problem'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'opts'}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'fd'}; {'id': '149', 'type': 'call', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': '_segyio'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'segyiofd'}; {'id': '153', 'type': 'argument_list', 'children': ['154', '158', '159']}; {'id': '154', 'type': 'call', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '158', 'type': 'string', 'children': [], 'value': "'w+'"}; {'id': '159', 'type': 'subscript', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'endians'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}; {'id': '163', 'type': 'call', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'fd'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'segymake'}; {'id': '167', 'type': 'argument_list', 'children': ['168', '174', '177', '185']}; {'id': '168', 'type': 'keyword_argument', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '170', 'type': 'call', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '172', 'type': 'argument_list', 'children': ['173']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '174', 'type': 'keyword_argument', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'tracecount'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'tracecount'}; {'id': '177', 'type': 'keyword_argument', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '179', 'type': 'call', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '181', 'type': 'argument_list', 'children': ['182']}; {'id': '182', 'type': 'attribute', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '185', 'type': 'keyword_argument', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'ext_headers'}; {'id': '187', 'type': 'call', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '189', 'type': 'argument_list', 'children': ['190']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'ext_headers'}; {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '194', 'type': 'call', 'children': ['195', '198']}; {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'segyio'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'SegyFile'}; {'id': '198', 'type': 'argument_list', 'children': ['199', '200', '206', '209', '217', '225']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'fd'}; {'id': '200', 'type': 'keyword_argument', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '202', 'type': 'call', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '206', 'type': 'keyword_argument', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'mode'}; {'id': '208', 'type': 'string', 'children': [], 'value': "'w+'"}; {'id': '209', 'type': 'keyword_argument', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '217', 'type': 'keyword_argument', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '219', 'type': 'call', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '225', 'type': 'keyword_argument', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}; {'id': '229', 'type': 'assignment', 'children': ['230', '233']}; {'id': '230', 'type': 'attribute', 'children': ['231', '232']}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': '_samples'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '234', 'type': 'if_statement', 'children': ['235', '239']}; {'id': '235', 'type': 'call', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'structured'}; {'id': '237', 'type': 'argument_list', 'children': ['238']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '239', 'type': 'block', 'children': ['240', '253', '264']}; {'id': '240', 'type': 'expression_statement', 'children': ['241']}; {'id': '241', 'type': 'assignment', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'sorting'}; {'id': '243', 'type': 'conditional_expression', 'children': ['244', '247', '252'], 'value': 'if'}; {'id': '244', 'type': 'attribute', 'children': ['245', '246']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'sorting'}; {'id': '247', 'type': 'call', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'hasattr'}; {'id': '249', 'type': 'argument_list', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '251', 'type': 'string', 'children': [], 'value': "'sorting'"}; {'id': '252', 'type': 'None', 'children': []}; {'id': '253', 'type': 'if_statement', 'children': ['254', '257']}; {'id': '254', 'type': 'comparison_operator', 'children': ['255', '256'], 'value': 'is'}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'sorting'}; {'id': '256', 'type': 'None', 'children': []}; {'id': '257', 'type': 'block', 'children': ['258']}; {'id': '258', 'type': 'expression_statement', 'children': ['259']}; {'id': '259', 'type': 'assignment', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'sorting'}; {'id': '261', 'type': 'attribute', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'TraceSortingFormat'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'INLINE_SORTING'}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}; {'id': '265', 'type': 'call', 'children': ['266', '269']}; {'id': '266', 'type': 'attribute', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'interpret'}; {'id': '269', 'type': 'argument_list', 'children': ['270', '273', '276', '279']}; {'id': '270', 'type': 'attribute', 'children': ['271', '272']}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'ilines'}; {'id': '273', 'type': 'attribute', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'xlines'}; {'id': '276', 'type': 'attribute', 'children': ['277', '278']}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'offsets'}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'sorting'}; {'id': '280', 'type': 'expression_statement', 'children': ['281']}; {'id': '281', 'type': 'assignment', 'children': ['282', '287']}; {'id': '282', 'type': 'subscript', 'children': ['283', '286']}; {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '286', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '287', 'type': 'call', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'default_text_header'}; {'id': '289', 'type': 'argument_list', 'children': ['290', '293', '296']}; {'id': '290', 'type': 'attribute', 'children': ['291', '292']}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': '_il'}; {'id': '293', 'type': 'attribute', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '295', 'type': 'identifier', 'children': [], 'value': '_xl'}; {'id': '296', 'type': 'attribute', 'children': ['297', '300']}; {'id': '297', 'type': 'attribute', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'segyio'}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'TraceField'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '301', 'type': 'if_statement', 'children': ['302', '308', '320']}; {'id': '302', 'type': 'comparison_operator', 'children': ['303', '307'], 'value': '=='}; {'id': '303', 'type': 'call', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '305', 'type': 'argument_list', 'children': ['306']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '307', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '308', 'type': 'block', 'children': ['309']}; {'id': '309', 'type': 'expression_statement', 'children': ['310']}; {'id': '310', 'type': 'assignment', 'children': ['311', '312']}; {'id': '311', 'type': 'identifier', 'children': [], 'value': 'interval'}; {'id': '312', 'type': 'call', 'children': ['313', '314']}; {'id': '313', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '314', 'type': 'argument_list', 'children': ['315']}; {'id': '315', 'type': 'binary_operator', 'children': ['316', '319'], 'value': '*'}; {'id': '316', 'type': 'subscript', 'children': ['317', '318']}; {'id': '317', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '318', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '319', 'type': 'integer', 'children': [], 'value': '1000'}; {'id': '320', 'type': 'else_clause', 'children': ['321']}; {'id': '321', 'type': 'block', 'children': ['322']}; {'id': '322', 'type': 'expression_statement', 'children': ['323']}; {'id': '323', 'type': 'assignment', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'interval'}; {'id': '325', 'type': 'call', 'children': ['326', '327']}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '327', 'type': 'argument_list', 'children': ['328']}; {'id': '328', 'type': 'binary_operator', 'children': ['329', '337'], 'value': '*'}; {'id': '329', 'type': '()', 'children': ['330']}; {'id': '330', 'type': 'binary_operator', 'children': ['331', '334'], 'value': '-'}; {'id': '331', 'type': 'subscript', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '333', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '334', 'type': 'subscript', 'children': ['335', '336']}; {'id': '335', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '336', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '337', 'type': 'integer', 'children': [], 'value': '1000'}; {'id': '338', 'type': 'expression_statement', 'children': ['339']}; {'id': '339', 'type': 'call', 'children': ['340', '345']}; {'id': '340', 'type': 'attribute', 'children': ['341', '344']}; {'id': '341', 'type': 'attribute', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '343', 'type': 'identifier', 'children': [], 'value': 'bin'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '345', 'type': 'argument_list', 'children': ['346', '349', '352', '355', '358', '364', '370', '378']}; {'id': '346', 'type': 'keyword_argument', 'children': ['347', '348']}; {'id': '347', 'type': 'identifier', 'children': [], 'value': 'ntrpr'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'tracecount'}; {'id': '349', 'type': 'keyword_argument', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'nart'}; {'id': '351', 'type': 'identifier', 'children': [], 'value': 'tracecount'}; {'id': '352', 'type': 'keyword_argument', 'children': ['353', '354']}; {'id': '353', 'type': 'identifier', 'children': [], 'value': 'hdt'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'interval'}; {'id': '355', 'type': 'keyword_argument', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'dto'}; {'id': '357', 'type': 'identifier', 'children': [], 'value': 'interval'}; {'id': '358', 'type': 'keyword_argument', 'children': ['359', '360']}; {'id': '359', 'type': 'identifier', 'children': [], 'value': 'hns'}; {'id': '360', 'type': 'call', 'children': ['361', '362']}; {'id': '361', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '362', 'type': 'argument_list', 'children': ['363']}; {'id': '363', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '364', 'type': 'keyword_argument', 'children': ['365', '366']}; {'id': '365', 'type': 'identifier', 'children': [], 'value': 'nso'}; {'id': '366', 'type': 'call', 'children': ['367', '368']}; {'id': '367', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '368', 'type': 'argument_list', 'children': ['369']}; {'id': '369', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '370', 'type': 'keyword_argument', 'children': ['371', '372']}; {'id': '371', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '372', 'type': 'call', 'children': ['373', '374']}; {'id': '373', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '374', 'type': 'argument_list', 'children': ['375']}; {'id': '375', 'type': 'attribute', 'children': ['376', '377']}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'spec'}; {'id': '377', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '378', 'type': 'keyword_argument', 'children': ['379', '380']}; {'id': '379', 'type': 'identifier', 'children': [], 'value': 'exth'}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'ext_headers'}; {'id': '381', 'type': 'return_statement', 'children': ['382']}; {'id': '382', 'type': 'identifier', 'children': [], 'value': 'f'} | def create(filename, spec):
from . import _segyio
if not structured(spec):
tracecount = spec.tracecount
else:
tracecount = len(spec.ilines) * len(spec.xlines) * len(spec.offsets)
ext_headers = spec.ext_headers if hasattr(spec, 'ext_headers') else 0
samples = numpy.asarray(spec.samples)
endians = {
'lsb': 256,
'little': 256,
'msb': 0,
'big': 0,
}
endian = spec.endian if hasattr(spec, 'endian') else 'big'
if endian is None:
endian = 'big'
if endian not in endians:
problem = 'unknown endianness {}, expected one of: '
opts = ' '.join(endians.keys())
raise ValueError(problem.format(endian) + opts)
fd = _segyio.segyiofd(str(filename), 'w+', endians[endian])
fd.segymake(
samples = len(samples),
tracecount = tracecount,
format = int(spec.format),
ext_headers = int(ext_headers),
)
f = segyio.SegyFile(fd,
filename = str(filename),
mode = 'w+',
iline = int(spec.iline),
xline = int(spec.xline),
endian = endian,
)
f._samples = samples
if structured(spec):
sorting = spec.sorting if hasattr(spec, 'sorting') else None
if sorting is None:
sorting = TraceSortingFormat.INLINE_SORTING
f.interpret(spec.ilines, spec.xlines, spec.offsets, sorting)
f.text[0] = default_text_header(f._il, f._xl, segyio.TraceField.offset)
if len(samples) == 1:
interval = int(samples[0] * 1000)
else:
interval = int((samples[1] - samples[0]) * 1000)
f.bin.update(
ntrpr = tracecount,
nart = tracecount,
hdt = interval,
dto = interval,
hns = len(samples),
nso = len(samples),
format = int(spec.format),
exth = ext_headers,
)
return f |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'rotation'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '7', 'type': 'string', 'children': [], 'value': "'fast'"}; {'id': '8', 'type': 'block', 'children': ['9', '19', '43', '86', '92', '111', '131', '169']}; {'id': '9', 'type': 'if_statement', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'unstructured'}; {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'raise_statement', 'children': ['15']}; {'id': '15', 'type': 'call', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '17', 'type': 'argument_list', 'children': ['18']}; {'id': '18', 'type': 'string', 'children': [], 'value': '"Rotation requires a structured file"'}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '22', 'type': 'dictionary', 'children': ['23', '28', '33', '38']}; {'id': '23', 'type': 'pair', 'children': ['24', '25']}; {'id': '24', 'type': 'string', 'children': [], 'value': "'fast'"}; {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'fast'}; {'id': '28', 'type': 'pair', 'children': ['29', '30']}; {'id': '29', 'type': 'string', 'children': [], 'value': "'slow'"}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'slow'}; {'id': '33', 'type': 'pair', 'children': ['34', '35']}; {'id': '34', 'type': 'string', 'children': [], 'value': "'iline'"}; {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '38', 'type': 'pair', 'children': ['39', '40']}; {'id': '39', 'type': 'string', 'children': [], 'value': "'xline'"}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '43', 'type': 'if_statement', 'children': ['44', '47']}; {'id': '44', 'type': 'comparison_operator', 'children': ['45', '46'], 'value': 'not'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '47', 'type': 'block', 'children': ['48', '57', '75']}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}; {'id': '49', 'type': 'assignment', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '51', 'type': 'call', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}; {'id': '53', 'type': 'string', 'children': [], 'value': '"Unknown line {}"'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'solution'}; {'id': '60', 'type': 'call', 'children': ['61', '64']}; {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'string', 'children': [], 'value': '"Must be any of: {}"'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'call', 'children': ['71', '74']}; {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '74', 'type': 'argument_list', 'children': []}; {'id': '75', 'type': 'raise_statement', 'children': ['76']}; {'id': '76', 'type': 'call', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}; {'id': '79', 'type': 'call', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}; {'id': '81', 'type': 'string', 'children': [], 'value': "'{} {}'"}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '83', 'type': 'argument_list', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'solution'}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'l'}; {'id': '89', 'type': 'subscript', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}; {'id': '93', 'type': 'assignment', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'origin'}; {'id': '95', 'type': 'subscript', 'children': ['96', '101', '106']}; {'id': '96', 'type': 'subscript', 'children': ['97', '100']}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '100', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '101', 'type': 'attribute', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'segyio'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'su'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'cdpx'}; {'id': '106', 'type': 'attribute', 'children': ['107', '110']}; {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'segyio'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'su'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'cdpy'}; {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '116']}; {'id': '113', 'type': 'pattern_list', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'cdpx'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'cdpy'}; {'id': '116', 'type': 'expression_list', 'children': ['117', '124']}; {'id': '117', 'type': 'subscript', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'origin'}; {'id': '119', 'type': 'attribute', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'segyio'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'su'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'cdpx'}; {'id': '124', 'type': 'subscript', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'origin'}; {'id': '126', 'type': 'attribute', 'children': ['127', '130']}; {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'segyio'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'su'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'cdpy'}; {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'rot'}; {'id': '134', 'type': 'call', 'children': ['135', '140']}; {'id': '135', 'type': 'attribute', 'children': ['136', '139']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'xfd'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'rotation'}; {'id': '140', 'type': 'argument_list', 'children': ['141', '145', '148', '154']}; {'id': '141', 'type': 'call', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'l'}; {'id': '145', 'type': 'attribute', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'l'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'stride'}; {'id': '148', 'type': 'call', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '150', 'type': 'argument_list', 'children': ['151']}; {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'offsets'}; {'id': '154', 'type': 'call', 'children': ['155', '158']}; {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'fromiter'}; {'id': '158', 'type': 'argument_list', 'children': ['159', '164']}; {'id': '159', 'type': 'call', 'children': ['160', '163']}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'l'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '163', 'type': 'argument_list', 'children': []}; {'id': '164', 'type': 'keyword_argument', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'intc'}; {'id': '169', 'type': 'return_statement', 'children': ['170']}; {'id': '170', 'type': 'expression_list', 'children': ['171', '172', '173']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'rot'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'cdpx'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'cdpy'} | def rotation(f, line = 'fast'):
if f.unstructured:
raise ValueError("Rotation requires a structured file")
lines = { 'fast': f.fast,
'slow': f.slow,
'iline': f.iline,
'xline': f.xline,
}
if line not in lines:
error = "Unknown line {}".format(line)
solution = "Must be any of: {}".format(' '.join(lines.keys()))
raise ValueError('{} {}'.format(error, solution))
l = lines[line]
origin = f.header[0][segyio.su.cdpx, segyio.su.cdpy]
cdpx, cdpy = origin[segyio.su.cdpx], origin[segyio.su.cdpy]
rot = f.xfd.rotation( len(l),
l.stride,
len(f.offsets),
np.fromiter(l.keys(), dtype = np.intc) )
return rot, cdpx, cdpy |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'from_array3D'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '17', '20']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '8', 'type': 'integer', 'children': [], 'value': '189'}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '11', 'type': 'integer', 'children': [], 'value': '193'}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'SegySampleFormat'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'IBM_FLOAT_4_BYTE'}; {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'dt'}; {'id': '19', 'type': 'integer', 'children': [], 'value': '4000'}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'delrt'}; {'id': '22', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '23', 'type': 'block', 'children': ['24', '33', '42', '61']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}; {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'asarray'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'dimensions'}; {'id': '36', 'type': 'call', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}; {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '42', 'type': 'if_statement', 'children': ['43', '46']}; {'id': '43', 'type': 'comparison_operator', 'children': ['44', '45'], 'value': '!='}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'dimensions'}; {'id': '45', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '46', 'type': 'block', 'children': ['47', '56']}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'problem'}; {'id': '50', 'type': 'call', 'children': ['51', '54']}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'string', 'children': [], 'value': '"Expected 3 dimensions, {} was given"'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'dimensions'}; {'id': '56', 'type': 'raise_statement', 'children': ['57']}; {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'problem'}; {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'call', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'from_array'}; {'id': '64', 'type': 'argument_list', 'children': ['65', '66', '67', '70', '73', '76', '79']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '67', 'type': 'keyword_argument', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '70', 'type': 'keyword_argument', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '73', 'type': 'keyword_argument', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '76', 'type': 'keyword_argument', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'dt'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'dt'}; {'id': '79', 'type': 'keyword_argument', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'delrt'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'delrt'} | def from_array3D(filename, data, iline=189,
xline=193,
format=SegySampleFormat.IBM_FLOAT_4_BYTE,
dt=4000,
delrt=0):
data = np.asarray(data)
dimensions = len(data.shape)
if dimensions != 3:
problem = "Expected 3 dimensions, {} was given".format(dimensions)
raise ValueError(problem)
from_array(filename, data, iline=iline, xline=xline, format=format,
dt=dt,
delrt=delrt) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'open'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'mode'}; {'id': '7', 'type': 'string', 'children': [], 'value': '"r"'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '10', 'type': 'integer', 'children': [], 'value': '189'}; {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '13', 'type': 'integer', 'children': [], 'value': '193'}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'strict'}; {'id': '16', 'type': 'True', 'children': []}; {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'ignore_geometry'}; {'id': '19', 'type': 'False', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '22', 'type': 'string', 'children': [], 'value': "'big'"}; {'id': '23', 'type': 'block', 'children': ['24', '49', '65', '99', '104', '120', '126', '134', '161', '224', '229']}; {'id': '24', 'type': 'if_statement', 'children': ['25', '28']}; {'id': '25', 'type': 'comparison_operator', 'children': ['26', '27'], 'value': 'in'}; {'id': '26', 'type': 'string', 'children': [], 'value': "'w'"}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'mode'}; {'id': '28', 'type': 'block', 'children': ['29', '33', '37']}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'problem'}; {'id': '32', 'type': 'string', 'children': [], 'value': "'w in mode would truncate the file'"}; {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'solution'}; {'id': '36', 'type': 'string', 'children': [], 'value': "'use r+ to open in read-write'"}; {'id': '37', 'type': 'raise_statement', 'children': ['38']}; {'id': '38', 'type': 'call', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}; {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'string', 'children': [], 'value': "', '"}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '45', 'type': 'argument_list', 'children': ['46']}; {'id': '46', 'type': 'tuple', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'problem'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'solution'}; {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'endians'}; {'id': '52', 'type': 'dictionary', 'children': ['53', '56', '59', '62']}; {'id': '53', 'type': 'pair', 'children': ['54', '55']}; {'id': '54', 'type': 'string', 'children': [], 'value': "'little'"}; {'id': '55', 'type': 'integer', 'children': [], 'value': '256'}; {'id': '56', 'type': 'pair', 'children': ['57', '58']}; {'id': '57', 'type': 'string', 'children': [], 'value': "'lsb'"}; {'id': '58', 'type': 'integer', 'children': [], 'value': '256'}; {'id': '59', 'type': 'pair', 'children': ['60', '61']}; {'id': '60', 'type': 'string', 'children': [], 'value': "'big'"}; {'id': '61', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '62', 'type': 'pair', 'children': ['63', '64']}; {'id': '63', 'type': 'string', 'children': [], 'value': "'msb'"}; {'id': '64', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '65', 'type': 'if_statement', 'children': ['66', '69']}; {'id': '66', 'type': 'comparison_operator', 'children': ['67', '68'], 'value': 'not'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'endians'}; {'id': '69', 'type': 'block', 'children': ['70', '74', '87']}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}; {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'problem'}; {'id': '73', 'type': 'string', 'children': [], 'value': "'unknown endianness {}, expected one of: '"}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}; {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'opts'}; {'id': '77', 'type': 'call', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}; {'id': '79', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'endians'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '86', 'type': 'argument_list', 'children': []}; {'id': '87', 'type': 'raise_statement', 'children': ['88']}; {'id': '88', 'type': 'call', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}; {'id': '91', 'type': 'binary_operator', 'children': ['92', '98'], 'value': '+'}; {'id': '92', 'type': 'call', 'children': ['93', '96']}; {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'problem'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'opts'}; {'id': '99', 'type': 'import_from_statement', 'children': ['100', '102']}; {'id': '100', 'type': 'relative_import', 'children': ['101']}; {'id': '101', 'type': 'import_prefix', 'children': []}; {'id': '102', 'type': 'dotted_name', 'children': ['103']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': '_segyio'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}; {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'fd'}; {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': '_segyio'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'segyiofd'}; {'id': '111', 'type': 'argument_list', 'children': ['112', '116', '117']}; {'id': '112', 'type': 'call', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'mode'}; {'id': '117', 'type': 'subscript', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'endians'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}; {'id': '121', 'type': 'call', 'children': ['122', '125']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'fd'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'segyopen'}; {'id': '125', 'type': 'argument_list', 'children': []}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}; {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'metrics'}; {'id': '129', 'type': 'call', 'children': ['130', '133']}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'fd'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'metrics'}; {'id': '133', 'type': 'argument_list', 'children': []}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '137', 'type': 'call', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'segyio'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'SegyFile'}; {'id': '141', 'type': 'argument_list', 'children': ['142', '143', '149', '152', '155', '158']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'fd'}; {'id': '143', 'type': 'keyword_argument', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '145', 'type': 'call', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '149', 'type': 'keyword_argument', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'mode'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'mode'}; {'id': '152', 'type': 'keyword_argument', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '155', 'type': 'keyword_argument', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '158', 'type': 'keyword_argument', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'endian'}; {'id': '161', 'type': 'try_statement', 'children': ['162', '215']}; {'id': '162', 'type': 'block', 'children': ['163', '179', '193', '199']}; {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'dt'}; {'id': '166', 'type': 'binary_operator', 'children': ['167', '178'], 'value': '/'}; {'id': '167', 'type': 'call', 'children': ['168', '173']}; {'id': '168', 'type': 'attribute', 'children': ['169', '172']}; {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'segyio'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'tools'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'dt'}; {'id': '173', 'type': 'argument_list', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '175', 'type': 'keyword_argument', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'fallback_dt'}; {'id': '177', 'type': 'float', 'children': [], 'value': '4000.0'}; {'id': '178', 'type': 'float', 'children': [], 'value': '1000.0'}; {'id': '179', 'type': 'expression_statement', 'children': ['180']}; {'id': '180', 'type': 'assignment', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 't0'}; {'id': '182', 'type': 'subscript', 'children': ['183', '188']}; {'id': '183', 'type': 'subscript', 'children': ['184', '187']}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'header'}; {'id': '187', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '188', 'type': 'attribute', 'children': ['189', '192']}; {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'segyio'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'TraceField'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'DelayRecordingTime'}; {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '196', 'type': 'subscript', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'metrics'}; {'id': '198', 'type': 'string', 'children': [], 'value': "'samplecount'"}; {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'assignment', 'children': ['201', '204']}; {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': '_samples'}; {'id': '204', 'type': 'binary_operator', 'children': ['205', '214'], 'value': '+'}; {'id': '205', 'type': '()', 'children': ['206']}; {'id': '206', 'type': 'binary_operator', 'children': ['207', '213'], 'value': '*'}; {'id': '207', 'type': 'call', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'numpy'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'arange'}; {'id': '211', 'type': 'argument_list', 'children': ['212']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'dt'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 't0'}; {'id': '215', 'type': 'except_clause', 'children': ['216']}; {'id': '216', 'type': 'block', 'children': ['217', '223']}; {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'call', 'children': ['219', '222']}; {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'close'}; {'id': '222', 'type': 'argument_list', 'children': []}; {'id': '223', 'type': 'raise_statement', 'children': []}; {'id': '224', 'type': 'if_statement', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'ignore_geometry'}; {'id': '226', 'type': 'block', 'children': ['227']}; {'id': '227', 'type': 'return_statement', 'children': ['228']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '229', 'type': 'return_statement', 'children': ['230']}; {'id': '230', 'type': 'call', 'children': ['231', '232']}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'infer_geometry'}; {'id': '232', 'type': 'argument_list', 'children': ['233', '234', '235', '236', '237']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'metrics'}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'iline'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'xline'}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'strict'} | def open(filename, mode="r", iline = 189,
xline = 193,
strict = True,
ignore_geometry = False,
endian = 'big'):
if 'w' in mode:
problem = 'w in mode would truncate the file'
solution = 'use r+ to open in read-write'
raise ValueError(', '.join((problem, solution)))
endians = {
'little': 256,
'lsb': 256,
'big': 0,
'msb': 0,
}
if endian not in endians:
problem = 'unknown endianness {}, expected one of: '
opts = ' '.join(endians.keys())
raise ValueError(problem.format(endian) + opts)
from . import _segyio
fd = _segyio.segyiofd(str(filename), mode, endians[endian])
fd.segyopen()
metrics = fd.metrics()
f = segyio.SegyFile(fd,
filename = str(filename),
mode = mode,
iline = iline,
xline = xline,
endian = endian,
)
try:
dt = segyio.tools.dt(f, fallback_dt = 4000.0) / 1000.0
t0 = f.header[0][segyio.TraceField.DelayRecordingTime]
samples = metrics['samplecount']
f._samples = (numpy.arange(samples) * dt) + t0
except:
f.close()
raise
if ignore_geometry:
return f
return infer_geometry(f, metrics, iline, xline, strict) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'calc_min_interval'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'alpha'}; {'id': '6', 'type': 'block', 'children': ['7', '14', '20', '34', '40', '54', '71', '80', '86', '94']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '12', 'type': 'argument_list', 'children': ['13']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}; {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'cred_mass'}; {'id': '17', 'type': 'binary_operator', 'children': ['18', '19'], 'value': '-'}; {'id': '18', 'type': 'float', 'children': [], 'value': '1.0'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'alpha'}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}; {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'interval_idx_inc'}; {'id': '23', 'type': 'call', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '25', 'type': 'argument_list', 'children': ['26']}; {'id': '26', 'type': 'call', 'children': ['27', '30']}; {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'floor'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}; {'id': '31', 'type': 'binary_operator', 'children': ['32', '33'], 'value': '*'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'cred_mass'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}; {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'n_intervals'}; {'id': '37', 'type': 'binary_operator', 'children': ['38', '39'], 'value': '-'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'interval_idx_inc'}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'interval_width'}; {'id': '43', 'type': 'binary_operator', 'children': ['44', '49'], 'value': '-'}; {'id': '44', 'type': 'subscript', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '46', 'type': 'slice', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'interval_idx_inc'}; {'id': '48', 'type': 'colon', 'children': []}; {'id': '49', 'type': 'subscript', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '51', 'type': 'slice', 'children': ['52', '53']}; {'id': '52', 'type': 'colon', 'children': []}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'n_intervals'}; {'id': '54', 'type': 'if_statement', 'children': ['55', '61']}; {'id': '55', 'type': 'comparison_operator', 'children': ['56', '60'], 'value': '=='}; {'id': '56', 'type': 'call', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'interval_width'}; {'id': '60', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '61', 'type': 'block', 'children': ['62', '67']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}; {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'print_'}; {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'string', 'children': [], 'value': "'Too few elements for interval calculation'"}; {'id': '67', 'type': 'return_statement', 'children': ['68']}; {'id': '68', 'type': 'list', 'children': ['69', '70'], 'value': '[None, None]'}; {'id': '69', 'type': 'None', 'children': []}; {'id': '70', 'type': 'None', 'children': []}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'min_idx'}; {'id': '74', 'type': 'call', 'children': ['75', '78']}; {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'argmin'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'interval_width'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'hdi_min'}; {'id': '83', 'type': 'subscript', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'min_idx'}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'hdi_max'}; {'id': '89', 'type': 'subscript', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '91', 'type': 'binary_operator', 'children': ['92', '93'], 'value': '+'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'min_idx'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'interval_idx_inc'}; {'id': '94', 'type': 'return_statement', 'children': ['95']}; {'id': '95', 'type': 'list', 'children': ['96', '97'], 'value': '[hdi_min, hdi_max]'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'hdi_min'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'hdi_max'} | def calc_min_interval(x, alpha):
n = len(x)
cred_mass = 1.0 - alpha
interval_idx_inc = int(np.floor(cred_mass * n))
n_intervals = n - interval_idx_inc
interval_width = x[interval_idx_inc:] - x[:n_intervals]
if len(interval_width) == 0:
print_('Too few elements for interval calculation')
return [None, None]
min_idx = np.argmin(interval_width)
hdi_min = x[min_idx]
hdi_max = x[min_idx + interval_idx_inc]
return [hdi_min, hdi_max] |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_compute_gas_price'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'probabilities'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'desired_probability'}; {'id': '6', 'type': 'block', 'children': ['7', '13', '20', '48']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'first'}; {'id': '10', 'type': 'subscript', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'probabilities'}; {'id': '12', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'last'}; {'id': '16', 'type': 'subscript', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'probabilities'}; {'id': '18', 'type': 'unary_operator', 'children': ['19'], 'value': '-'}; {'id': '19', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '20', 'type': 'if_statement', 'children': ['21', '26', '34']}; {'id': '21', 'type': 'comparison_operator', 'children': ['22', '23'], 'value': '>='}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'desired_probability'}; {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'first'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '26', 'type': 'block', 'children': ['27']}; {'id': '27', 'type': 'return_statement', 'children': ['28']}; {'id': '28', 'type': 'call', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}; {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'first'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'gas_price'}; {'id': '34', 'type': 'elif_clause', 'children': ['35', '40']}; {'id': '35', 'type': 'comparison_operator', 'children': ['36', '37'], 'value': '<='}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'desired_probability'}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'last'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '40', 'type': 'block', 'children': ['41']}; {'id': '41', 'type': 'return_statement', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'last'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'gas_price'}; {'id': '48', 'type': 'for_statement', 'children': ['49', '52', '57', '132']}; {'id': '49', 'type': 'pattern_list', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'left'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'right'}; {'id': '52', 'type': 'call', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'sliding_window'}; {'id': '54', 'type': 'argument_list', 'children': ['55', '56']}; {'id': '55', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'probabilities'}; {'id': '57', 'type': 'block', 'children': ['58', '78', '86', '96', '102', '112', '130']}; {'id': '58', 'type': 'if_statement', 'children': ['59', '64', '66']}; {'id': '59', 'type': 'comparison_operator', 'children': ['60', '61'], 'value': '<'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'desired_probability'}; {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'right'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '64', 'type': 'block', 'children': ['65']}; {'id': '65', 'type': 'continue_statement', 'children': []}; {'id': '66', 'type': 'elif_clause', 'children': ['67', '72']}; {'id': '67', 'type': 'comparison_operator', 'children': ['68', '69'], 'value': '>'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'desired_probability'}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'left'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '72', 'type': 'block', 'children': ['73']}; {'id': '73', 'type': 'raise_statement', 'children': ['74']}; {'id': '74', 'type': 'call', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}; {'id': '77', 'type': 'string', 'children': [], 'value': "'Invariant'"}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}; {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'adj_prob'}; {'id': '81', 'type': 'binary_operator', 'children': ['82', '83'], 'value': '-'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'desired_probability'}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'right'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'window_size'}; {'id': '89', 'type': 'binary_operator', 'children': ['90', '93'], 'value': '-'}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'left'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'right'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}; {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '99', 'type': 'binary_operator', 'children': ['100', '101'], 'value': '/'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'adj_prob'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'window_size'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'gas_window_size'}; {'id': '105', 'type': 'binary_operator', 'children': ['106', '109'], 'value': '-'}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'left'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'gas_price'}; {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'right'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'gas_price'}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}; {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'gas_price'}; {'id': '115', 'type': 'call', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'call', 'children': ['119', '122']}; {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'math'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'ceil'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}; {'id': '123', 'type': 'binary_operator', 'children': ['124', '127'], 'value': '+'}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'right'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'gas_price'}; {'id': '127', 'type': 'binary_operator', 'children': ['128', '129'], 'value': '*'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'gas_window_size'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '130', 'type': 'return_statement', 'children': ['131']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'gas_price'}; {'id': '132', 'type': 'else_clause', 'children': ['133']}; {'id': '133', 'type': 'block', 'children': ['134']}; {'id': '134', 'type': 'raise_statement', 'children': ['135']}; {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'string', 'children': [], 'value': "'Invariant'"} | def _compute_gas_price(probabilities, desired_probability):
first = probabilities[0]
last = probabilities[-1]
if desired_probability >= first.prob:
return int(first.gas_price)
elif desired_probability <= last.prob:
return int(last.gas_price)
for left, right in sliding_window(2, probabilities):
if desired_probability < right.prob:
continue
elif desired_probability > left.prob:
raise Exception('Invariant')
adj_prob = desired_probability - right.prob
window_size = left.prob - right.prob
position = adj_prob / window_size
gas_window_size = left.gas_price - right.gas_price
gas_price = int(math.ceil(right.gas_price + gas_window_size * position))
return gas_price
else:
raise Exception('Invariant') |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'generate_X_grid'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '8', 'type': 'integer', 'children': [], 'value': '100'}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'meshgrid'}; {'id': '11', 'type': 'False', 'children': []}; {'id': '12', 'type': 'block', 'children': ['13', '24', '38']}; {'id': '13', 'type': 'if_statement', 'children': ['14', '18']}; {'id': '14', 'type': 'not_operator', 'children': ['15']}; {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': '_is_fitted'}; {'id': '18', 'type': 'block', 'children': ['19']}; {'id': '19', 'type': 'raise_statement', 'children': ['20']}; {'id': '20', 'type': 'call', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'string', 'children': [], 'value': "'GAM has not been fitted. Call fit first.'"}; {'id': '24', 'type': 'if_statement', 'children': ['25', '32']}; {'id': '25', 'type': 'attribute', 'children': ['26', '31']}; {'id': '26', 'type': 'subscript', 'children': ['27', '30']}; {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'isintercept'}; {'id': '32', 'type': 'block', 'children': ['33']}; {'id': '33', 'type': 'raise_statement', 'children': ['34']}; {'id': '34', 'type': 'call', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '36', 'type': 'argument_list', 'children': ['37']}; {'id': '37', 'type': 'string', 'children': [], 'value': "'cannot create grid for intercept term'"}; {'id': '38', 'type': 'if_statement', 'children': ['39', '46', '116', '221']}; {'id': '39', 'type': 'attribute', 'children': ['40', '45']}; {'id': '40', 'type': 'subscript', 'children': ['41', '44']}; {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'istensor'}; {'id': '46', 'type': 'block', 'children': ['47', '51', '83', '96']}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'Xs'}; {'id': '50', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '51', 'type': 'for_statement', 'children': ['52', '53', '58']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'term_'}; {'id': '53', 'type': 'subscript', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '58', 'type': 'block', 'children': ['59']}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'call', 'children': ['61', '64']}; {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'Xs'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'linspace'}; {'id': '69', 'type': 'argument_list', 'children': ['70', '75', '80']}; {'id': '70', 'type': 'subscript', 'children': ['71', '74']}; {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'term_'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'edge_knots_'}; {'id': '74', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '75', 'type': 'subscript', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'term_'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'edge_knots_'}; {'id': '79', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '80', 'type': 'keyword_argument', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'num'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'Xs'}; {'id': '86', 'type': 'call', 'children': ['87', '90']}; {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'meshgrid'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '93']}; {'id': '91', 'type': 'list_splat', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'Xs'}; {'id': '93', 'type': 'keyword_argument', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'indexing'}; {'id': '95', 'type': 'string', 'children': [], 'value': "'ij'"}; {'id': '96', 'type': 'if_statement', 'children': ['97', '98', '104']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'meshgrid'}; {'id': '98', 'type': 'block', 'children': ['99']}; {'id': '99', 'type': 'return_statement', 'children': ['100']}; {'id': '100', 'type': 'call', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'Xs'}; {'id': '104', 'type': 'else_clause', 'children': ['105']}; {'id': '105', 'type': 'block', 'children': ['106']}; {'id': '106', 'type': 'return_statement', 'children': ['107']}; {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': '_flatten_mesh'}; {'id': '111', 'type': 'argument_list', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'Xs'}; {'id': '113', 'type': 'keyword_argument', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '116', 'type': 'elif_clause', 'children': ['117', '126']}; {'id': '117', 'type': 'call', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'hasattr'}; {'id': '119', 'type': 'argument_list', 'children': ['120', '125']}; {'id': '120', 'type': 'subscript', 'children': ['121', '124']}; {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '125', 'type': 'string', 'children': [], 'value': "'edge_knots_'"}; {'id': '126', 'type': 'block', 'children': ['127', '156', '162', '177', '191', '219']}; {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'assignment', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '130', 'type': 'call', 'children': ['131', '134']}; {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'linspace'}; {'id': '134', 'type': 'argument_list', 'children': ['135', '144', '153']}; {'id': '135', 'type': 'subscript', 'children': ['136', '143']}; {'id': '136', 'type': 'attribute', 'children': ['137', '142']}; {'id': '137', 'type': 'subscript', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'edge_knots_'}; {'id': '143', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '144', 'type': 'subscript', 'children': ['145', '152']}; {'id': '145', 'type': 'attribute', 'children': ['146', '151']}; {'id': '146', 'type': 'subscript', 'children': ['147', '150']}; {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'edge_knots_'}; {'id': '152', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '153', 'type': 'keyword_argument', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'num'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '156', 'type': 'if_statement', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'meshgrid'}; {'id': '158', 'type': 'block', 'children': ['159']}; {'id': '159', 'type': 'return_statement', 'children': ['160']}; {'id': '160', 'type': 'tuple', 'children': ['161']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}; {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'X'}; {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'zeros'}; {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'tuple', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '172', 'type': 'subscript', 'children': ['173', '176']}; {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'statistics_'}; {'id': '176', 'type': 'string', 'children': [], 'value': "'m_features'"}; {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '190']}; {'id': '179', 'type': 'subscript', 'children': ['180', '181', '183']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'X'}; {'id': '181', 'type': 'slice', 'children': ['182']}; {'id': '182', 'type': 'colon', 'children': []}; {'id': '183', 'type': 'attribute', 'children': ['184', '189']}; {'id': '184', 'type': 'subscript', 'children': ['185', '188']}; {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '191', 'type': 'if_statement', 'children': ['192', '204']}; {'id': '192', 'type': 'comparison_operator', 'children': ['193', '203'], 'value': 'is'}; {'id': '193', 'type': 'call', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '195', 'type': 'argument_list', 'children': ['196', '201', '202']}; {'id': '196', 'type': 'subscript', 'children': ['197', '200']}; {'id': '197', 'type': 'attribute', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '201', 'type': 'string', 'children': [], 'value': "'by'"}; {'id': '202', 'type': 'None', 'children': []}; {'id': '203', 'type': 'None', 'children': []}; {'id': '204', 'type': 'block', 'children': ['205']}; {'id': '205', 'type': 'expression_statement', 'children': ['206']}; {'id': '206', 'type': 'assignment', 'children': ['207', '218']}; {'id': '207', 'type': 'subscript', 'children': ['208', '209', '211']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'X'}; {'id': '209', 'type': 'slice', 'children': ['210']}; {'id': '210', 'type': 'colon', 'children': []}; {'id': '211', 'type': 'attribute', 'children': ['212', '217']}; {'id': '212', 'type': 'subscript', 'children': ['213', '216']}; {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'by'}; {'id': '218', 'type': 'float', 'children': [], 'value': '1.'}; {'id': '219', 'type': 'return_statement', 'children': ['220']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'X'}; {'id': '221', 'type': 'else_clause', 'children': ['222']}; {'id': '222', 'type': 'block', 'children': ['223']}; {'id': '223', 'type': 'raise_statement', 'children': ['224']}; {'id': '224', 'type': 'call', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'TypeError'}; {'id': '226', 'type': 'argument_list', 'children': ['227']}; {'id': '227', 'type': 'call', 'children': ['228', '231']}; {'id': '228', 'type': 'attribute', 'children': ['229', '230']}; {'id': '229', 'type': 'string', 'children': [], 'value': "'Unexpected term type: {}'"}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '231', 'type': 'argument_list', 'children': ['232']}; {'id': '232', 'type': 'subscript', 'children': ['233', '236']}; {'id': '233', 'type': 'attribute', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'term'} | def generate_X_grid(self, term, n=100, meshgrid=False):
if not self._is_fitted:
raise AttributeError('GAM has not been fitted. Call fit first.')
if self.terms[term].isintercept:
raise ValueError('cannot create grid for intercept term')
if self.terms[term].istensor:
Xs = []
for term_ in self.terms[term]:
Xs.append(np.linspace(term_.edge_knots_[0],
term_.edge_knots_[1],
num=n))
Xs = np.meshgrid(*Xs, indexing='ij')
if meshgrid:
return tuple(Xs)
else:
return self._flatten_mesh(Xs, term=term)
elif hasattr(self.terms[term], 'edge_knots_'):
x = np.linspace(self.terms[term].edge_knots_[0],
self.terms[term].edge_knots_[1],
num=n)
if meshgrid:
return (x,)
X = np.zeros((n, self.statistics_['m_features']))
X[:, self.terms[term].feature] = x
if getattr(self.terms[term], 'by', None) is not None:
X[:, self.terms[term].by] = 1.
return X
else:
raise TypeError('Unexpected term type: {}'.format(self.terms[term])) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'build_from_info'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '29']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '10', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '11', 'type': 'for_statement', 'children': ['12', '13', '16']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'term_info'}; {'id': '13', 'type': 'subscript', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '15', 'type': 'string', 'children': [], 'value': "'terms'"}; {'id': '16', 'type': 'block', 'children': ['17']}; {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'call', 'children': ['19', '22']}; {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'call', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'SplineTerm'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'build_from_info'}; {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'term_info'}; {'id': '29', 'type': 'return_statement', 'children': ['30']}; {'id': '30', 'type': 'call', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '32', 'type': 'argument_list', 'children': ['33']}; {'id': '33', 'type': 'list_splat', 'children': ['34']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'terms'} | def build_from_info(cls, info):
terms = []
for term_info in info['terms']:
terms.append(SplineTerm.build_from_info(term_info))
return cls(*terms) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_kate_imports'}; {'id': '3', 'type': 'parameters', 'children': ['4', '7']}; {'id': '4', 'type': 'default_parameter', 'children': ['5', '6']}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'add_imports'}; {'id': '6', 'type': 'tuple', 'children': []}; {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'remove_imports'}; {'id': '9', 'type': 'tuple', 'children': []}; {'id': '10', 'type': 'block', 'children': ['11', '19', '27', '35', '43', '90', '99', '114', '178']}; {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'document'}; {'id': '14', 'type': 'call', 'children': ['15', '18']}; {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'kate'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'activeDocument'}; {'id': '18', 'type': 'argument_list', 'children': []}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'view'}; {'id': '22', 'type': 'call', 'children': ['23', '26']}; {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'document'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'activeView'}; {'id': '26', 'type': 'argument_list', 'children': []}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '30', 'type': 'call', 'children': ['31', '34']}; {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'view'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'cursorPosition'}; {'id': '34', 'type': 'argument_list', 'children': []}; {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'selection'}; {'id': '38', 'type': 'call', 'children': ['39', '42']}; {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'view'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'selectionRange'}; {'id': '42', 'type': 'argument_list', 'children': []}; {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '46', 'type': 'call', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'SortImports'}; {'id': '48', 'type': 'argument_list', 'children': ['49', '56', '59', '62']}; {'id': '49', 'type': 'keyword_argument', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'file_contents'}; {'id': '51', 'type': 'call', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'document'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '55', 'type': 'argument_list', 'children': []}; {'id': '56', 'type': 'keyword_argument', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'add_imports'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'add_imports'}; {'id': '59', 'type': 'keyword_argument', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'remove_imports'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'remove_imports'}; {'id': '62', 'type': 'keyword_argument', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'settings_path'}; {'id': '64', 'type': 'call', 'children': ['65', '70']}; {'id': '65', 'type': 'attribute', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'dirname'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}; {'id': '71', 'type': 'call', 'children': ['72', '77']}; {'id': '72', 'type': 'attribute', 'children': ['73', '76']}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'abspath'}; {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'call', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '80', 'type': 'argument_list', 'children': ['81']}; {'id': '81', 'type': 'call', 'children': ['82', '89']}; {'id': '82', 'type': 'attribute', 'children': ['83', '88']}; {'id': '83', 'type': 'call', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'document'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '87', 'type': 'argument_list', 'children': []}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '89', 'type': 'argument_list', 'children': []}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}; {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'document'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'setText'}; {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'output'}; {'id': '99', 'type': 'expression_statement', 'children': ['100']}; {'id': '100', 'type': 'call', 'children': ['101', '104']}; {'id': '101', 'type': 'attribute', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'setLine'}; {'id': '104', 'type': 'argument_list', 'children': ['105']}; {'id': '105', 'type': 'binary_operator', 'children': ['106', '111'], 'value': '+'}; {'id': '106', 'type': 'call', 'children': ['107', '110']}; {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '110', 'type': 'argument_list', 'children': []}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'length_change'}; {'id': '114', 'type': 'if_statement', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'selection'}; {'id': '116', 'type': 'block', 'children': ['117', '125', '140', '148', '163', '171']}; {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '120', 'type': 'call', 'children': ['121', '124']}; {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'selection'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '124', 'type': 'argument_list', 'children': []}; {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'call', 'children': ['127', '130']}; {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'setLine'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}; {'id': '131', 'type': 'binary_operator', 'children': ['132', '137'], 'value': '+'}; {'id': '132', 'type': 'call', 'children': ['133', '136']}; {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '136', 'type': 'argument_list', 'children': []}; {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'length_change'}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}; {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '143', 'type': 'call', 'children': ['144', '147']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'selection'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '147', 'type': 'argument_list', 'children': []}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}; {'id': '149', 'type': 'call', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'setLine'}; {'id': '153', 'type': 'argument_list', 'children': ['154']}; {'id': '154', 'type': 'binary_operator', 'children': ['155', '160'], 'value': '+'}; {'id': '155', 'type': 'call', 'children': ['156', '159']}; {'id': '156', 'type': 'attribute', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '159', 'type': 'argument_list', 'children': []}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'length_change'}; {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '168']}; {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'selection'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'setRange'}; {'id': '168', 'type': 'argument_list', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'call', 'children': ['173', '176']}; {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'view'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'setSelection'}; {'id': '176', 'type': 'argument_list', 'children': ['177']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'selection'}; {'id': '178', 'type': 'expression_statement', 'children': ['179']}; {'id': '179', 'type': 'call', 'children': ['180', '183']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'view'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'setCursorPosition'}; {'id': '183', 'type': 'argument_list', 'children': ['184']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'position'} | def sort_kate_imports(add_imports=(), remove_imports=()):
document = kate.activeDocument()
view = document.activeView()
position = view.cursorPosition()
selection = view.selectionRange()
sorter = SortImports(file_contents=document.text(), add_imports=add_imports, remove_imports=remove_imports,
settings_path=os.path.dirname(os.path.abspath(str(document.url().path()))))
document.setText(sorter.output)
position.setLine(position.line() + sorter.length_change)
if selection:
start = selection.start()
start.setLine(start.line() + sorter.length_change)
end = selection.end()
end.setLine(end.line() + sorter.length_change)
selection.setRange(start, end)
view.setSelection(selection)
view.setCursorPosition(position) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_line'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'type', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '7', 'type': 'block', 'children': ['8', '18', '24']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '11', 'type': 'subscript', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'in_lines'}; {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}; {'id': '19', 'type': 'augmented_assignment', 'children': ['20', '23'], 'value': '+='}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '23', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '24', 'type': 'return_statement', 'children': ['25']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'line'} | def _get_line(self) -> str:
line = self.in_lines[self.index]
self.index += 1
return line |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '22', '24']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_add_comments'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '17']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'typed_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'comments'}; {'id': '7', 'type': 'type', 'children': ['8']}; {'id': '8', 'type': 'generic_type', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'Optional'}; {'id': '10', 'type': 'type_parameter', 'children': ['11']}; {'id': '11', 'type': 'type', 'children': ['12']}; {'id': '12', 'type': 'generic_type', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'Sequence'}; {'id': '14', 'type': 'type_parameter', 'children': ['15']}; {'id': '15', 'type': 'type', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '17', 'type': 'typed_default_parameter', 'children': ['18', '19', '21']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'original_string'}; {'id': '19', 'type': 'type', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '21', 'type': 'string', 'children': [], 'value': '""'}; {'id': '22', 'type': 'type', 'children': ['23']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '24', 'type': 'block', 'children': ['25', '41']}; {'id': '25', 'type': 'if_statement', 'children': ['26', '31']}; {'id': '26', 'type': 'subscript', 'children': ['27', '30']}; {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '30', 'type': 'string', 'children': [], 'value': "'ignore_comments'"}; {'id': '31', 'type': 'block', 'children': ['32']}; {'id': '32', 'type': 'return_statement', 'children': ['33']}; {'id': '33', 'type': 'subscript', 'children': ['34', '40']}; {'id': '34', 'type': 'call', 'children': ['35', '38']}; {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': '_strip_comments'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'original_string'}; {'id': '40', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '41', 'type': 'if_statement', 'children': ['42', '44', '47']}; {'id': '42', 'type': 'not_operator', 'children': ['43']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'comments'}; {'id': '44', 'type': 'block', 'children': ['45']}; {'id': '45', 'type': 'return_statement', 'children': ['46']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'original_string'}; {'id': '47', 'type': 'else_clause', 'children': ['48']}; {'id': '48', 'type': 'block', 'children': ['49']}; {'id': '49', 'type': 'return_statement', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'string', 'children': [], 'value': '"{0}{1} {2}"'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '54', 'type': 'argument_list', 'children': ['55', '63', '68']}; {'id': '55', 'type': 'subscript', 'children': ['56', '62']}; {'id': '56', 'type': 'call', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': '_strip_comments'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'original_string'}; {'id': '62', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '63', 'type': 'subscript', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '67', 'type': 'string', 'children': [], 'value': "'comment_prefix'"}; {'id': '68', 'type': 'call', 'children': ['69', '72']}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'string', 'children': [], 'value': '"; "'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '72', 'type': 'argument_list', 'children': ['73']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'comments'} | def _add_comments(
self,
comments: Optional[Sequence[str]],
original_string: str = ""
) -> str:
if self.config['ignore_comments']:
return self._strip_comments(original_string)[0]
if not comments:
return original_string
else:
return "{0}{1} {2}".format(self._strip_comments(original_string)[0],
self.config['comment_prefix'],
"; ".join(comments)) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_wrap'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'typed_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '7', 'type': 'type', 'children': ['8']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '9', 'type': 'type', 'children': ['10']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '11', 'type': 'block', 'children': ['12', '20', '370']}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}; {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'wrap_mode'}; {'id': '15', 'type': 'subscript', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '19', 'type': 'string', 'children': [], 'value': "'multi_line_output'"}; {'id': '20', 'type': 'if_statement', 'children': ['21', '37', '333']}; {'id': '21', 'type': 'boolean_operator', 'children': ['22', '32'], 'value': 'and'}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '27'], 'value': '>'}; {'id': '23', 'type': 'call', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '25', 'type': 'argument_list', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '27', 'type': 'subscript', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '31', 'type': 'string', 'children': [], 'value': "'line_length'"}; {'id': '32', 'type': 'comparison_operator', 'children': ['33', '34'], 'value': '!='}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'wrap_mode'}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'WrapModes'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'NOQA'}; {'id': '37', 'type': 'block', 'children': ['38', '42', '46']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}; {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'line_without_comment'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'comment'}; {'id': '45', 'type': 'None', 'children': []}; {'id': '46', 'type': 'if_statement', 'children': ['47', '56']}; {'id': '47', 'type': 'comparison_operator', 'children': ['48', '49', '52'], 'value': 'in'}; {'id': '48', 'type': 'string', 'children': [], 'value': "'\n line_without_comment, comment = line.split('"}; {'id': '49', 'type': 'ERROR', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'for'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'splitter'}; {'id': '52', 'type': 'tuple', 'children': ['53', '54', '55']}; {'id': '53', 'type': 'string', 'children': [], 'value': '"import "'}; {'id': '54', 'type': 'string', 'children': [], 'value': '"."'}; {'id': '55', 'type': 'string', 'children': [], 'value': '"as "'}; {'id': '56', 'type': 'block', 'children': ['57', '70']}; {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'exp'}; {'id': '60', 'type': 'binary_operator', 'children': ['61', '69'], 'value': '+'}; {'id': '61', 'type': 'binary_operator', 'children': ['62', '63'], 'value': '+'}; {'id': '62', 'type': 'string', 'children': [], 'value': 'r"\\b"'}; {'id': '63', 'type': 'call', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'escape'}; {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'splitter'}; {'id': '69', 'type': 'string', 'children': [], 'value': 'r"\\b"'}; {'id': '70', 'type': 'if_statement', 'children': ['71', '90']}; {'id': '71', 'type': 'boolean_operator', 'children': ['72', '79'], 'value': 'and'}; {'id': '72', 'type': 'call', 'children': ['73', '76']}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'search'}; {'id': '76', 'type': 'argument_list', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'exp'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'line_without_comment'}; {'id': '79', 'type': 'not_operator', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '88']}; {'id': '81', 'type': 'attribute', 'children': ['82', '87']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'line_without_comment'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'strip'}; {'id': '86', 'type': 'argument_list', 'children': []}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'splitter'}; {'id': '90', 'type': 'block', 'children': ['91', '101', '115', '159', '171', '195', '321']}; {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'line_parts'}; {'id': '94', 'type': 'call', 'children': ['95', '98']}; {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '98', 'type': 'argument_list', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'exp'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'line_without_comment'}; {'id': '101', 'type': 'if_statement', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'comment'}; {'id': '103', 'type': 'block', 'children': ['104']}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}; {'id': '105', 'type': 'assignment', 'children': ['106', '110', '114']}; {'id': '106', 'type': 'subscript', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'line_parts'}; {'id': '108', 'type': 'unary_operator', 'children': ['109'], 'value': '-'}; {'id': '109', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '110', 'type': 'ERROR', 'children': ['111', '113']}; {'id': '111', 'type': 'interpolation', 'children': ['112']}; {'id': '112', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'next_line'}; {'id': '114', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '115', 'type': 'while_statement', 'children': ['116', '138']}; {'id': '116', 'type': 'boolean_operator', 'children': ['117', '137'], 'value': 'and'}; {'id': '117', 'type': 'comparison_operator', 'children': ['118', '125'], 'value': '>'}; {'id': '118', 'type': '()', 'children': ['119']}; {'id': '119', 'type': 'binary_operator', 'children': ['120', '124'], 'value': '+'}; {'id': '120', 'type': 'call', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '124', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '125', 'type': '()', 'children': ['126']}; {'id': '126', 'type': 'boolean_operator', 'children': ['127', '132'], 'value': 'or'}; {'id': '127', 'type': 'subscript', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '131', 'type': 'string', 'children': [], 'value': "'wrap_length'"}; {'id': '132', 'type': 'subscript', 'children': ['133', '136']}; {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '136', 'type': 'string', 'children': [], 'value': "'line_length'"}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'line_parts'}; {'id': '138', 'type': 'block', 'children': ['139', '150']}; {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'call', 'children': ['141', '144']}; {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'next_line'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}; {'id': '145', 'type': 'call', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'line_parts'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '149', 'type': 'argument_list', 'children': []}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}; {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'splitter'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'line_parts'}; {'id': '159', 'type': 'if_statement', 'children': ['160', '162']}; {'id': '160', 'type': 'not_operator', 'children': ['161']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '162', 'type': 'block', 'children': ['163']}; {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '166', 'type': 'call', 'children': ['167', '170']}; {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'next_line'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '170', 'type': 'argument_list', 'children': []}; {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'cont_line'}; {'id': '174', 'type': 'call', 'children': ['175', '178']}; {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': '_wrap'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}; {'id': '179', 'type': 'binary_operator', 'children': ['180', '185'], 'value': '+'}; {'id': '180', 'type': 'subscript', 'children': ['181', '184']}; {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '184', 'type': 'string', 'children': [], 'value': "'indent'"}; {'id': '185', 'type': 'call', 'children': ['186', '194']}; {'id': '186', 'type': 'attribute', 'children': ['187', '193']}; {'id': '187', 'type': 'call', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'splitter'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'next_line'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'lstrip'}; {'id': '194', 'type': 'argument_list', 'children': []}; {'id': '195', 'type': 'if_statement', 'children': ['196', '201']}; {'id': '196', 'type': 'subscript', 'children': ['197', '200']}; {'id': '197', 'type': 'attribute', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '200', 'type': 'string', 'children': [], 'value': "'use_parentheses'"}; {'id': '201', 'type': 'block', 'children': ['202', '238', '249', '312']}; {'id': '202', 'type': 'expression_statement', 'children': ['203']}; {'id': '203', 'type': 'assignment', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'output'}; {'id': '205', 'type': 'call', 'children': ['206', '209']}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}; {'id': '207', 'type': 'string', 'children': [], 'value': '"{0}{1}({2}{3}{4}{5})"'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '209', 'type': 'argument_list', 'children': ['210', '211', '212', '215', '216', '224']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'splitter'}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'line_separator'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'cont_line'}; {'id': '216', 'type': 'conditional_expression', 'children': ['217', '218', '223'], 'value': 'if'}; {'id': '217', 'type': 'string', 'children': [], 'value': '","'}; {'id': '218', 'type': 'subscript', 'children': ['219', '222']}; {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '222', 'type': 'string', 'children': [], 'value': "'include_trailing_comma'"}; {'id': '223', 'type': 'string', 'children': [], 'value': '""'}; {'id': '224', 'type': 'conditional_expression', 'children': ['225', '228', '237'], 'value': 'if'}; {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'line_separator'}; {'id': '228', 'type': 'comparison_operator', 'children': ['229', '230'], 'value': 'in'}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'wrap_mode'}; {'id': '230', 'type': 'set', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'WrapModes'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'VERTICAL_HANGING_INDENT'}; {'id': '234', 'type': 'attribute', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'WrapModes'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'VERTICAL_GRID_GROUPED'}; {'id': '237', 'type': 'string', 'children': [], 'value': '""'}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}; {'id': '239', 'type': 'assignment', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '241', 'type': 'call', 'children': ['242', '245']}; {'id': '242', 'type': 'attribute', 'children': ['243', '244']}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'output'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'attribute', 'children': ['247', '248']}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'line_separator'}; {'id': '249', 'type': 'if_statement', 'children': ['250', '270']}; {'id': '250', 'type': 'boolean_operator', 'children': ['251', '261'], 'value': 'and'}; {'id': '251', 'type': 'comparison_operator', 'children': ['252', '257'], 'value': 'in'}; {'id': '252', 'type': 'subscript', 'children': ['253', '256']}; {'id': '253', 'type': 'attribute', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '256', 'type': 'string', 'children': [], 'value': "'comment_prefix'"}; {'id': '257', 'type': 'subscript', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '259', 'type': 'unary_operator', 'children': ['260'], 'value': '-'}; {'id': '260', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '261', 'type': 'call', 'children': ['262', '268']}; {'id': '262', 'type': 'attribute', 'children': ['263', '267']}; {'id': '263', 'type': 'subscript', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '265', 'type': 'unary_operator', 'children': ['266'], 'value': '-'}; {'id': '266', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '268', 'type': 'argument_list', 'children': ['269']}; {'id': '269', 'type': 'string', 'children': [], 'value': "')'"}; {'id': '270', 'type': 'block', 'children': ['271', '290']}; {'id': '271', 'type': 'expression_statement', 'children': ['272']}; {'id': '272', 'type': 'assignment', 'children': ['273', '276']}; {'id': '273', 'type': 'pattern_list', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'comment'}; {'id': '276', 'type': 'call', 'children': ['277', '283']}; {'id': '277', 'type': 'attribute', 'children': ['278', '282']}; {'id': '278', 'type': 'subscript', 'children': ['279', '280']}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '280', 'type': 'unary_operator', 'children': ['281'], 'value': '-'}; {'id': '281', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '283', 'type': 'argument_list', 'children': ['284', '289']}; {'id': '284', 'type': 'subscript', 'children': ['285', '288']}; {'id': '285', 'type': 'attribute', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '288', 'type': 'string', 'children': [], 'value': "'comment_prefix'"}; {'id': '289', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '290', 'type': 'expression_statement', 'children': ['291']}; {'id': '291', 'type': 'assignment', 'children': ['292', '296']}; {'id': '292', 'type': 'subscript', 'children': ['293', '294']}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '294', 'type': 'unary_operator', 'children': ['295'], 'value': '-'}; {'id': '295', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '296', 'type': 'binary_operator', 'children': ['297', '306'], 'value': '+'}; {'id': '297', 'type': 'binary_operator', 'children': ['298', '301'], 'value': '+'}; {'id': '298', 'type': 'binary_operator', 'children': ['299', '300'], 'value': '+'}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '300', 'type': 'string', 'children': [], 'value': "')'"}; {'id': '301', 'type': 'subscript', 'children': ['302', '305']}; {'id': '302', 'type': 'attribute', 'children': ['303', '304']}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '305', 'type': 'string', 'children': [], 'value': "'comment_prefix'"}; {'id': '306', 'type': 'subscript', 'children': ['307', '308']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'comment'}; {'id': '308', 'type': 'slice', 'children': ['309', '310']}; {'id': '309', 'type': 'colon', 'children': []}; {'id': '310', 'type': 'unary_operator', 'children': ['311'], 'value': '-'}; {'id': '311', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '312', 'type': 'return_statement', 'children': ['313']}; {'id': '313', 'type': 'call', 'children': ['314', '319']}; {'id': '314', 'type': 'attribute', 'children': ['315', '318']}; {'id': '315', 'type': 'attribute', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '317', 'type': 'identifier', 'children': [], 'value': 'line_separator'}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '319', 'type': 'argument_list', 'children': ['320']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '321', 'type': 'return_statement', 'children': ['322']}; {'id': '322', 'type': 'call', 'children': ['323', '326']}; {'id': '323', 'type': 'attribute', 'children': ['324', '325']}; {'id': '324', 'type': 'string', 'children': [], 'value': '"{0}{1}\\\\{2}{3}"'}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '326', 'type': 'argument_list', 'children': ['327', '328', '329', '332']}; {'id': '327', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'splitter'}; {'id': '329', 'type': 'attribute', 'children': ['330', '331']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '331', 'type': 'identifier', 'children': [], 'value': 'line_separator'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'cont_line'}; {'id': '333', 'type': 'elif_clause', 'children': ['334', '352', '369']}; {'id': '334', 'type': 'boolean_operator', 'children': ['335', '345'], 'value': 'and'}; {'id': '335', 'type': 'comparison_operator', 'children': ['336', '340'], 'value': '>'}; {'id': '336', 'type': 'call', 'children': ['337', '338']}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '338', 'type': 'argument_list', 'children': ['339']}; {'id': '339', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '340', 'type': 'subscript', 'children': ['341', '344']}; {'id': '341', 'type': 'attribute', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '343', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '344', 'type': 'string', 'children': [], 'value': "'line_length'"}; {'id': '345', 'type': 'comparison_operator', 'children': ['346', '347'], 'value': '=='}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'wrap_mode'}; {'id': '347', 'type': 'attribute', 'children': ['348', '351']}; {'id': '348', 'type': 'attribute', 'children': ['349', '350']}; {'id': '349', 'type': 'identifier', 'children': [], 'value': 'settings'}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'WrapModes'}; {'id': '351', 'type': 'identifier', 'children': [], 'value': 'NOQA'}; {'id': '352', 'type': 'ERROR', 'children': ['353', '360']}; {'id': '353', 'type': 'ERROR', 'children': ['354', '355', '357', '359']}; {'id': '354', 'type': 'string', 'children': [], 'value': '"\n return "'}; {'id': '355', 'type': 'set', 'children': ['356']}; {'id': '356', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '357', 'type': 'set', 'children': ['358']}; {'id': '358', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '359', 'type': 'identifier', 'children': [], 'value': 'NOQA'}; {'id': '360', 'type': 'call', 'children': ['361', '362']}; {'id': '361', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '362', 'type': 'argument_list', 'children': ['363', '364']}; {'id': '363', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '364', 'type': 'subscript', 'children': ['365', '368']}; {'id': '365', 'type': 'attribute', 'children': ['366', '367']}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '367', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '368', 'type': 'string', 'children': [], 'value': "'comment_prefix'"}; {'id': '369', 'type': 'block', 'children': [], 'value': ''}; {'id': '370', 'type': 'return_statement', 'children': ['371']}; {'id': '371', 'type': 'identifier', 'children': [], 'value': 'line'} | def _wrap(self, line: str) -> str:
wrap_mode = self.config['multi_line_output']
if len(line) > self.config['line_length'] and wrap_mode != WrapModes.NOQA:
line_without_comment = line
comment = None
if '
line_without_comment, comment = line.split('
for splitter in ("import ", ".", "as "):
exp = r"\b" + re.escape(splitter) + r"\b"
if re.search(exp, line_without_comment) and not line_without_comment.strip().startswith(splitter):
line_parts = re.split(exp, line_without_comment)
if comment:
line_parts[-1] = '{0}
next_line = []
while (len(line) + 2) > (self.config['wrap_length'] or self.config['line_length']) and line_parts:
next_line.append(line_parts.pop())
line = splitter.join(line_parts)
if not line:
line = next_line.pop()
cont_line = self._wrap(self.config['indent'] + splitter.join(next_line).lstrip())
if self.config['use_parentheses']:
output = "{0}{1}({2}{3}{4}{5})".format(
line, splitter, self.line_separator, cont_line,
"," if self.config['include_trailing_comma'] else "",
self.line_separator if wrap_mode in {WrapModes.VERTICAL_HANGING_INDENT,
WrapModes.VERTICAL_GRID_GROUPED}
else "")
lines = output.split(self.line_separator)
if self.config['comment_prefix'] in lines[-1] and lines[-1].endswith(')'):
line, comment = lines[-1].split(self.config['comment_prefix'], 1)
lines[-1] = line + ')' + self.config['comment_prefix'] + comment[:-1]
return self.line_separator.join(lines)
return "{0}{1}\\{2}{3}".format(line, splitter, self.line_separator, cont_line)
elif len(line) > self.config['line_length'] and wrap_mode == settings.WrapModes.NOQA:
if "
return "{0}{1} NOQA".format(line, self.config['comment_prefix'])
return line |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_formatter'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '5', 'type': 'block', 'children': ['6']}; {'id': '6', 'type': 'for_statement', 'children': ['7', '8', '12']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '8', 'type': 'call', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '10', 'type': 'argument_list', 'children': ['11']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': '_FORMATTERS'}; {'id': '12', 'type': 'block', 'children': ['13']}; {'id': '13', 'type': 'if_statement', 'children': ['14', '20']}; {'id': '14', 'type': 'call', 'children': ['15', '18']}; {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '18', 'type': 'argument_list', 'children': ['19']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '20', 'type': 'block', 'children': ['21']}; {'id': '21', 'type': 'return_statement', 'children': ['22']}; {'id': '22', 'type': 'subscript', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': '_FORMATTERS'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'k'} | def get_formatter(name):
for k in sorted(_FORMATTERS):
if k.startswith(name):
return _FORMATTERS[k] |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'call_once'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '5', 'type': 'block', 'children': ['6', '15', '35', '73', '79', '88', '100']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'argspec'}; {'id': '9', 'type': 'call', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'inspect'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'getargspec'}; {'id': '13', 'type': 'argument_list', 'children': ['14']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '15', 'type': 'if_statement', 'children': ['16', '27']}; {'id': '16', 'type': 'boolean_operator', 'children': ['17', '24'], 'value': 'or'}; {'id': '17', 'type': 'boolean_operator', 'children': ['18', '21'], 'value': 'or'}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'argspec'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'argspec'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'varargs'}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'argspec'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'keywords'}; {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'raise_statement', 'children': ['29']}; {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '31', 'type': 'argument_list', 'children': ['32', '33', '34']}; {'id': '32', 'type': 'string', 'children': [], 'value': "'Can only decorate functions with no args'"}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'argspec'}; {'id': '35', 'type': 'decorated_definition', 'children': ['36', '43']}; {'id': '36', 'type': 'decorator', 'children': ['37']}; {'id': '37', 'type': 'call', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'functools'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'wraps'}; {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '43', 'type': 'function_definition', 'children': ['44', '45', '46']}; {'id': '44', 'type': 'function_name', 'children': [], 'value': '_wrapper'}; {'id': '45', 'type': 'parameters', 'children': []}; {'id': '46', 'type': 'block', 'children': ['47', '69']}; {'id': '47', 'type': 'if_statement', 'children': ['48', '54']}; {'id': '48', 'type': 'not_operator', 'children': ['49']}; {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': '_wrapper'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'HasRun'}; {'id': '53', 'type': 'argument_list', 'children': []}; {'id': '54', 'type': 'block', 'children': ['55', '61']}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'call', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': '_wrapper'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'MarkAsRun'}; {'id': '60', 'type': 'argument_list', 'children': []}; {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '66']}; {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': '_wrapper'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'return_value'}; {'id': '66', 'type': 'call', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '68', 'type': 'argument_list', 'children': []}; {'id': '69', 'type': 'return_statement', 'children': ['70']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': '_wrapper'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'return_value'}; {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '78']}; {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': '_wrapper'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'has_run'}; {'id': '78', 'type': 'False', 'children': []}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '84']}; {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': '_wrapper'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'HasRun'}; {'id': '84', 'type': 'lambda', 'children': ['85']}; {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': '_wrapper'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'has_run'}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}; {'id': '89', 'type': 'assignment', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': '_wrapper'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'MarkAsRun'}; {'id': '93', 'type': 'lambda', 'children': ['94']}; {'id': '94', 'type': 'call', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'setattr'}; {'id': '96', 'type': 'argument_list', 'children': ['97', '98', '99']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': '_wrapper'}; {'id': '98', 'type': 'string', 'children': [], 'value': "'has_run'"}; {'id': '99', 'type': 'True', 'children': []}; {'id': '100', 'type': 'return_statement', 'children': ['101']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': '_wrapper'} | def call_once(func):
argspec = inspect.getargspec(func)
if argspec.args or argspec.varargs or argspec.keywords:
raise ValueError('Can only decorate functions with no args', func, argspec)
@functools.wraps(func)
def _wrapper():
if not _wrapper.HasRun():
_wrapper.MarkAsRun()
_wrapper.return_value = func()
return _wrapper.return_value
_wrapper.has_run = False
_wrapper.HasRun = lambda: _wrapper.has_run
_wrapper.MarkAsRun = lambda: setattr(_wrapper, 'has_run', True)
return _wrapper |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '19']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'paginate'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'model_class'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'order_by'}; {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'page_num'}; {'id': '9', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '12', 'type': 'integer', 'children': [], 'value': '100'}; {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'conditions'}; {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'default_parameter', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'settings'}; {'id': '18', 'type': 'None', 'children': []}; {'id': '19', 'type': 'block', 'children': ['20', '22', '32', '47', '73', '82', '86', '95', '101', '109', '119']}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}; {'id': '21', 'type': 'string', 'children': [], 'value': "'''\n Selects records and returns a single page of model instances.\n - `model_class`: the model class matching the query's table,\n or `None` for getting back instances of an ad-hoc model.\n - `order_by`: columns to use for sorting the query (contents of the ORDER BY clause).\n - `page_num`: the page number (1-based), or -1 to get the last page.\n - `page_size`: number of records to return per page.\n - `conditions`: optional SQL conditions (contents of the WHERE clause).\n - `settings`: query settings to send as HTTP GET parameters\n The result is a namedtuple containing `objects` (list), `number_of_objects`,\n `pages_total`, `number` (of the current page), and `page_size`.\n '''"}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '29', 'type': 'argument_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'model_class'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'conditions'}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'pages_total'}; {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'call', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'ceil'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}; {'id': '41', 'type': 'binary_operator', 'children': ['42', '43'], 'value': '/'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '43', 'type': 'call', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '45', 'type': 'argument_list', 'children': ['46']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '47', 'type': 'if_statement', 'children': ['48', '52', '61']}; {'id': '48', 'type': 'comparison_operator', 'children': ['49', '50'], 'value': '=='}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'page_num'}; {'id': '50', 'type': 'unary_operator', 'children': ['51'], 'value': '-'}; {'id': '51', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '52', 'type': 'block', 'children': ['53']}; {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'page_num'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '58', 'type': 'argument_list', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'pages_total'}; {'id': '60', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '61', 'type': 'elif_clause', 'children': ['62', '65']}; {'id': '62', 'type': 'comparison_operator', 'children': ['63', '64'], 'value': '<'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'page_num'}; {'id': '64', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'raise_statement', 'children': ['67']}; {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'binary_operator', 'children': ['71', '72'], 'value': '%'}; {'id': '71', 'type': 'string', 'children': [], 'value': "'Invalid page number: %d'"}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'page_num'}; {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '76', 'type': 'binary_operator', 'children': ['77', '81'], 'value': '*'}; {'id': '77', 'type': '()', 'children': ['78']}; {'id': '78', 'type': 'binary_operator', 'children': ['79', '80'], 'value': '-'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'page_num'}; {'id': '80', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}; {'id': '83', 'type': 'assignment', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '85', 'type': 'string', 'children': [], 'value': "'SELECT * FROM $table'"}; {'id': '86', 'type': 'if_statement', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'conditions'}; {'id': '88', 'type': 'block', 'children': ['89']}; {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'augmented_assignment', 'children': ['91', '92'], 'value': '+='}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '92', 'type': 'binary_operator', 'children': ['93', '94'], 'value': '+'}; {'id': '93', 'type': 'string', 'children': [], 'value': "' WHERE '"}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'conditions'}; {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'augmented_assignment', 'children': ['97', '98'], 'value': '+='}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '98', 'type': 'binary_operator', 'children': ['99', '100'], 'value': '%'}; {'id': '99', 'type': 'string', 'children': [], 'value': "' ORDER BY %s'"}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'order_by'}; {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'augmented_assignment', 'children': ['103', '104'], 'value': '+='}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '104', 'type': 'binary_operator', 'children': ['105', '106'], 'value': '%'}; {'id': '105', 'type': 'string', 'children': [], 'value': "' LIMIT %d, %d'"}; {'id': '106', 'type': 'tuple', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '112', 'type': 'call', 'children': ['113', '116']}; {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': '_substitute'}; {'id': '116', 'type': 'argument_list', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'model_class'}; {'id': '119', 'type': 'return_statement', 'children': ['120']}; {'id': '120', 'type': 'call', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'Page'}; {'id': '122', 'type': 'argument_list', 'children': ['123', '139', '142', '145', '148']}; {'id': '123', 'type': 'keyword_argument', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'objects'}; {'id': '125', 'type': 'conditional_expression', 'children': ['126', '137', '138'], 'value': 'if'}; {'id': '126', 'type': 'call', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}; {'id': '129', 'type': 'call', 'children': ['130', '133']}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'select'}; {'id': '133', 'type': 'argument_list', 'children': ['134', '135', '136']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'model_class'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'settings'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '138', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '139', 'type': 'keyword_argument', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'number_of_objects'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '142', 'type': 'keyword_argument', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'pages_total'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'pages_total'}; {'id': '145', 'type': 'keyword_argument', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'number'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'page_num'}; {'id': '148', 'type': 'keyword_argument', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'page_size'} | def paginate(self, model_class, order_by, page_num=1, page_size=100, conditions=None, settings=None):
'''
Selects records and returns a single page of model instances.
- `model_class`: the model class matching the query's table,
or `None` for getting back instances of an ad-hoc model.
- `order_by`: columns to use for sorting the query (contents of the ORDER BY clause).
- `page_num`: the page number (1-based), or -1 to get the last page.
- `page_size`: number of records to return per page.
- `conditions`: optional SQL conditions (contents of the WHERE clause).
- `settings`: query settings to send as HTTP GET parameters
The result is a namedtuple containing `objects` (list), `number_of_objects`,
`pages_total`, `number` (of the current page), and `page_size`.
'''
count = self.count(model_class, conditions)
pages_total = int(ceil(count / float(page_size)))
if page_num == -1:
page_num = max(pages_total, 1)
elif page_num < 1:
raise ValueError('Invalid page number: %d' % page_num)
offset = (page_num - 1) * page_size
query = 'SELECT * FROM $table'
if conditions:
query += ' WHERE ' + conditions
query += ' ORDER BY %s' % order_by
query += ' LIMIT %d, %d' % (offset, page_size)
query = self._substitute(query, model_class)
return Page(
objects=list(self.select(query, model_class, settings)) if count else [],
number_of_objects=count,
pages_total=pages_total,
number=page_num,
page_size=page_size
) |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'compute_memory_contents_under_schedule'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'schedule'}; {'id': '6', 'type': 'block', 'children': ['7', '15', '21', '25', '117']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'out_degree'}; {'id': '10', 'type': 'call', 'children': ['11', '14']}; {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': '_compute_initial_out_degree'}; {'id': '14', 'type': 'argument_list', 'children': []}; {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'curr_memory_contents'}; {'id': '18', 'type': 'call', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '20', 'type': 'argument_list', 'children': []}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'memory_contents_for_each_operation'}; {'id': '24', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '25', 'type': 'for_statement', 'children': ['26', '27', '28']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'operation_id'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'schedule'}; {'id': '28', 'type': 'block', 'children': ['29', '39', '55', '65', '88']}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'operation_name'}; {'id': '32', 'type': 'attribute', 'children': ['33', '38']}; {'id': '33', 'type': 'subscript', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': '_operations'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'operation_id'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '39', 'type': 'for_statement', 'children': ['40', '41', '47']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'output_name'}; {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'get_operation_output_names'}; {'id': '45', 'type': 'argument_list', 'children': ['46']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'operation_name'}; {'id': '47', 'type': 'block', 'children': ['48']}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}; {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'curr_memory_contents'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'output_name'}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'call', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'memory_contents_for_each_operation'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'frozenset'}; {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'curr_memory_contents'}; {'id': '65', 'type': 'for_statement', 'children': ['66', '67', '73']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'output_name'}; {'id': '67', 'type': 'call', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'get_operation_output_names'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'operation_name'}; {'id': '73', 'type': 'block', 'children': ['74']}; {'id': '74', 'type': 'if_statement', 'children': ['75', '80']}; {'id': '75', 'type': 'comparison_operator', 'children': ['76', '79'], 'value': '=='}; {'id': '76', 'type': 'subscript', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'out_degree'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'output_name'}; {'id': '79', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '80', 'type': 'block', 'children': ['81']}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'curr_memory_contents'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'remove'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'output_name'}; {'id': '88', 'type': 'for_statement', 'children': ['89', '90', '96']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'input_name'}; {'id': '90', 'type': 'call', 'children': ['91', '94']}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'get_operation_input_names'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'operation_name'}; {'id': '96', 'type': 'block', 'children': ['97', '103']}; {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'augmented_assignment', 'children': ['99', '102'], 'value': '-='}; {'id': '99', 'type': 'subscript', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'out_degree'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'input_name'}; {'id': '102', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '103', 'type': 'if_statement', 'children': ['104', '109']}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '108'], 'value': '=='}; {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'out_degree'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'input_name'}; {'id': '108', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}; {'id': '111', 'type': 'call', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'curr_memory_contents'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'remove'}; {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'input_name'}; {'id': '117', 'type': 'return_statement', 'children': ['118']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'memory_contents_for_each_operation'} | def compute_memory_contents_under_schedule(self, schedule):
out_degree = self._compute_initial_out_degree()
curr_memory_contents = set()
memory_contents_for_each_operation = []
for operation_id in schedule:
operation_name = self._operations[operation_id].name
for output_name in self.get_operation_output_names(operation_name):
curr_memory_contents.add(output_name)
memory_contents_for_each_operation.append(frozenset(curr_memory_contents))
for output_name in self.get_operation_output_names(operation_name):
if out_degree[output_name] == 0:
curr_memory_contents.remove(output_name)
for input_name in self.get_operation_input_names(operation_name):
out_degree[input_name] -= 1
if out_degree[input_name] == 0:
curr_memory_contents.remove(input_name)
return memory_contents_for_each_operation |
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{'id': '16', 'type': 'type', 'children': ['17']}; {'id': '17', 'type': 'string', 'children': [], 'value': "'SASdata'"}; {'id': '18', 'type': 'block', 'children': ['19', '23', '27', '117', '128', '147', '153', '157', '161', '177', '185', '192', '252']}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'outstr'}; {'id': '22', 'type': 'string', 'children': [], 'value': "''"}; {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '26', 'type': 'string', 'children': [], 'value': "''"}; {'id': '27', 'type': 'if_statement', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'if_statement', 'children': ['31', '36', '91']}; {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '33', 'type': 'argument_list', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '36', 'type': 'block', 'children': ['37', '46']}; {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'fn'}; {'id': '40', 'type': 'call', 'children': ['41', '44']}; {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'partition'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '46', 'type': 'if_statement', 'children': ['47', '52', '73']}; {'id': '47', 'type': 'comparison_operator', 'children': ['48', '51'], 'value': '=='}; {'id': '48', 'type': 'subscript', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'fn'}; {'id': '50', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '51', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '52', 'type': 'block', 'children': ['53', '59', '65']}; {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'libref'}; {'id': '56', 'type': 'subscript', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'fn'}; {'id': '58', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '62', 'type': 'subscript', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'fn'}; {'id': '64', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'outstr'}; {'id': '68', 'type': 'binary_operator', 'children': ['69', '70'], 'value': '%'}; {'id': '69', 'type': 'string', 'children': [], 'value': '"out=%s.%s"'}; {'id': '70', 'type': 'tuple', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'libref'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '73', 'type': 'else_clause', 'children': ['74']}; {'id': '74', 'type': 'block', 'children': ['75', '79', '85']}; {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'libref'}; {'id': '78', 'type': 'string', 'children': [], 'value': "''"}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '82', 'type': 'subscript', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'fn'}; {'id': '84', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'outstr'}; {'id': '88', 'type': 'binary_operator', 'children': ['89', '90'], 'value': '+'}; {'id': '89', 'type': 'string', 'children': [], 'value': '"out="'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '91', 'type': 'else_clause', 'children': ['92']}; {'id': '92', 'type': 'block', 'children': ['93', '99', '105']}; {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'libref'}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'libref'}; {'id': '99', 'type': 'expression_statement', 'children': ['100']}; {'id': '100', 'type': 'assignment', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'assignment', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'outstr'}; {'id': '108', 'type': 'binary_operator', 'children': ['109', '110'], 'value': '%'}; {'id': '109', 'type': 'string', 'children': [], 'value': '"out=%s.%s"'}; {'id': '110', 'type': 'tuple', 'children': ['111', '114']}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'libref'}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '117', 'type': 'if_statement', 'children': ['118', '121']}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'in'}; {'id': '119', 'type': 'string', 'children': [], 'value': "'options'"}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '121', 'type': 'block', 'children': ['122']}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '125', 'type': 'subscript', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '127', 'type': 'string', 'children': [], 'value': "'options'"}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}; {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '131', 'type': 'binary_operator', 'children': ['132', '133'], 'value': '%'}; {'id': '132', 'type': 'string', 'children': [], 'value': '"proc sort data=%s.%s%s %s %s ;\\n"'}; {'id': '133', 'type': 'tuple', 'children': ['134', '137', '140', '145', '146']}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'libref'}; {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '140', 'type': 'call', 'children': ['141', '144']}; {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': '_dsopts'}; {'id': '144', 'type': 'argument_list', 'children': []}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'outstr'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'augmented_assignment', 'children': ['149', '150'], 'value': '+='}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '150', 'type': 'binary_operator', 'children': ['151', '152'], 'value': '%'}; {'id': '151', 'type': 'string', 'children': [], 'value': '"by %s;"'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'by'}; {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'augmented_assignment', 'children': ['155', '156'], 'value': '+='}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '156', 'type': 'string', 'children': [], 'value': '"run\\n;"'}; {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'runcode'}; {'id': '160', 'type': 'True', 'children': []}; {'id': '161', 'type': 'if_statement', 'children': ['162', '167']}; {'id': '162', 'type': 'attribute', 'children': ['163', '166']}; {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'sas'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'nosub'}; {'id': '167', 'type': 'block', 'children': ['168', '173']}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}; {'id': '169', 'type': 'call', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'assignment', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'runcode'}; {'id': '176', 'type': 'False', 'children': []}; {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'll'}; {'id': '180', 'type': 'call', 'children': ['181', '184']}; {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': '_is_valid'}; {'id': '184', 'type': 'argument_list', 'children': []}; {'id': '185', 'type': 'if_statement', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'll'}; {'id': '187', 'type': 'block', 'children': ['188']}; {'id': '188', 'type': 'expression_statement', 'children': ['189']}; {'id': '189', 'type': 'assignment', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'runcode'}; {'id': '191', 'type': 'False', 'children': []}; {'id': '192', 'type': 'if_statement', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'runcode'}; {'id': '194', 'type': 'block', 'children': ['195', '207', '211', '236']}; {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'll'}; {'id': '198', 'type': 'call', 'children': ['199', '204']}; {'id': '199', 'type': 'attribute', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'sas'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'submit'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '206', 'type': 'string', 'children': [], 'value': '"text"'}; {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'assignment', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'elog'}; {'id': '210', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '211', 'type': 'for_statement', 'children': ['212', '213', '220']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '213', 'type': 'call', 'children': ['214', '219']}; {'id': '214', 'type': 'attribute', 'children': ['215', '218']}; {'id': '215', 'type': 'subscript', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'll'}; {'id': '217', 'type': 'string', 'children': [], 'value': "'LOG'"}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'splitlines'}; {'id': '219', 'type': 'argument_list', 'children': []}; {'id': '220', 'type': 'block', 'children': ['221']}; {'id': '221', 'type': 'if_statement', 'children': ['222', '228']}; {'id': '222', 'type': 'call', 'children': ['223', '226']}; {'id': '223', 'type': 'attribute', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '226', 'type': 'argument_list', 'children': ['227']}; {'id': '227', 'type': 'string', 'children': [], 'value': "'ERROR'"}; {'id': '228', 'type': 'block', 'children': ['229']}; {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'call', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'elog'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '234', 'type': 'argument_list', 'children': ['235']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '236', 'type': 'if_statement', 'children': ['237', '241']}; {'id': '237', 'type': 'call', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '239', 'type': 'argument_list', 'children': ['240']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'elog'}; {'id': '241', 'type': 'block', 'children': ['242']}; {'id': '242', 'type': 'raise_statement', 'children': ['243']}; {'id': '243', 'type': 'call', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'RuntimeError'}; {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'call', 'children': ['247', '250']}; {'id': '247', 'type': 'attribute', 'children': ['248', '249']}; {'id': '248', 'type': 'string', 'children': [], 'value': '"\\n"'}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '250', 'type': 'argument_list', 'children': ['251']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'elog'}; {'id': '252', 'type': 'if_statement', 'children': ['253', '254', '280']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '254', 'type': 'block', 'children': ['255']}; {'id': '255', 'type': 'if_statement', 'children': ['256', '262', '265']}; {'id': '256', 'type': 'not_operator', 'children': ['257']}; {'id': '257', 'type': 'call', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '259', 'type': 'argument_list', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '262', 'type': 'block', 'children': ['263']}; {'id': '263', 'type': 'return_statement', 'children': ['264']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '265', 'type': 'else_clause', 'children': ['266']}; {'id': '266', 'type': 'block', 'children': ['267']}; {'id': '267', 'type': 'return_statement', 'children': ['268']}; {'id': '268', 'type': 'call', 'children': ['269', '274']}; {'id': '269', 'type': 'attribute', 'children': ['270', '273']}; {'id': '270', 'type': 'attribute', 'children': ['271', '272']}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'sas'}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'sasdata'}; {'id': '274', 'type': 'argument_list', 'children': ['275', '276', '277']}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'libref'}; {'id': '277', 'type': 'attribute', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '280', 'type': 'else_clause', 'children': ['281']}; {'id': '281', 'type': 'block', 'children': ['282']}; {'id': '282', 'type': 'return_statement', 'children': ['283']}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'self'} | def sort(self, by: str, out: object = '', **kwargs) -> 'SASdata':
outstr = ''
options = ''
if out:
if isinstance(out, str):
fn = out.partition('.')
if fn[1] == '.':
libref = fn[0]
table = fn[2]
outstr = "out=%s.%s" % (libref, table)
else:
libref = ''
table = fn[0]
outstr = "out=" + table
else:
libref = out.libref
table = out.table
outstr = "out=%s.%s" % (out.libref, out.table)
if 'options' in kwargs:
options = kwargs['options']
code = "proc sort data=%s.%s%s %s %s ;\n" % (self.libref, self.table, self._dsopts(), outstr, options)
code += "by %s;" % by
code += "run\n;"
runcode = True
if self.sas.nosub:
print(code)
runcode = False
ll = self._is_valid()
if ll:
runcode = False
if runcode:
ll = self.sas.submit(code, "text")
elog = []
for line in ll['LOG'].splitlines():
if line.startswith('ERROR'):
elog.append(line)
if len(elog):
raise RuntimeError("\n".join(elog))
if out:
if not isinstance(out, str):
return out
else:
return self.sas.sasdata(table, libref, self.results)
else:
return self |
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '30']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'find_items'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18', '21', '24', '27']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'ID_ONLY'}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'depth'}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'SHALLOW'}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'additional_fields'}; {'id': '14', 'type': 'None', 'children': []}; {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'order_fields'}; {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'default_parameter', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'calendar_view'}; {'id': '20', 'type': 'None', 'children': []}; {'id': '21', 'type': 'default_parameter', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'default_parameter', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'max_items'}; {'id': '26', 'type': 'None', 'children': []}; {'id': '27', 'type': 'default_parameter', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '29', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '30', 'type': 'block', 'children': ['31', '45', '59', '73', '111', '130', '194', '216', '271']}; {'id': '31', 'type': 'if_statement', 'children': ['32', '35']}; {'id': '32', 'type': 'comparison_operator', 'children': ['33', '34'], 'value': 'not'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'SHAPE_CHOICES'}; {'id': '35', 'type': 'block', 'children': ['36']}; {'id': '36', 'type': 'raise_statement', 'children': ['37']}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'binary_operator', 'children': ['41', '42'], 'value': '%'}; {'id': '41', 'type': 'string', 'children': [], 'value': '"\'shape\' %s must be one of %s"'}; {'id': '42', 'type': 'tuple', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'SHAPE_CHOICES'}; {'id': '45', 'type': 'if_statement', 'children': ['46', '49']}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '48'], 'value': 'not'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'depth'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'ITEM_TRAVERSAL_CHOICES'}; {'id': '49', 'type': 'block', 'children': ['50']}; {'id': '50', 'type': 'raise_statement', 'children': ['51']}; {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'binary_operator', 'children': ['55', '56'], 'value': '%'}; {'id': '55', 'type': 'string', 'children': [], 'value': '"\'depth\' %s must be one of %s"'}; {'id': '56', 'type': 'tuple', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'depth'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'ITEM_TRAVERSAL_CHOICES'}; {'id': '59', 'type': 'if_statement', 'children': ['60', '64']}; {'id': '60', 'type': 'not_operator', 'children': ['61']}; {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'folders'}; {'id': '64', 'type': 'block', 'children': ['65', '72']}; {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'call', 'children': ['67', '70']}; {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}; {'id': '71', 'type': 'string', 'children': [], 'value': "'Folder list is empty'"}; {'id': '72', 'type': 'return_statement', 'children': []}; {'id': '73', 'type': 'if_statement', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'additional_fields'}; {'id': '75', 'type': 'block', 'children': ['76', '89']}; {'id': '76', 'type': 'for_statement', 'children': ['77', '78', '79']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'additional_fields'}; {'id': '79', 'type': 'block', 'children': ['80']}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'validate_item_field'}; {'id': '85', 'type': 'argument_list', 'children': ['86']}; {'id': '86', 'type': 'keyword_argument', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '89', 'type': 'for_statement', 'children': ['90', '91', '92']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'additional_fields'}; {'id': '92', 'type': 'block', 'children': ['93']}; {'id': '93', 'type': 'if_statement', 'children': ['94', '99']}; {'id': '94', 'type': 'attribute', 'children': ['95', '98']}; {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'is_complex'}; {'id': '99', 'type': 'block', 'children': ['100']}; {'id': '100', 'type': 'raise_statement', 'children': ['101']}; {'id': '101', 'type': 'call', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'binary_operator', 'children': ['105', '106'], 'value': '%'}; {'id': '105', 'type': 'string', 'children': [], 'value': '"find_items() does not support field \'%s\'. Use fetch() instead"'}; {'id': '106', 'type': 'attribute', 'children': ['107', '110']}; {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '111', 'type': 'if_statement', 'children': ['112', '122']}; {'id': '112', 'type': 'boolean_operator', 'children': ['113', '116'], 'value': 'and'}; {'id': '113', 'type': 'comparison_operator', 'children': ['114', '115'], 'value': 'is'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'calendar_view'}; {'id': '115', 'type': 'None', 'children': []}; {'id': '116', 'type': 'not_operator', 'children': ['117']}; {'id': '117', 'type': 'call', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '119', 'type': 'argument_list', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'calendar_view'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'CalendarView'}; {'id': '122', 'type': 'block', 'children': ['123']}; {'id': '123', 'type': 'raise_statement', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}; {'id': '127', 'type': 'binary_operator', 'children': ['128', '129'], 'value': '%'}; {'id': '128', 'type': 'string', 'children': [], 'value': '"\'calendar_view\' %s must be a CalendarView instance"'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'calendar_view'}; {'id': '130', 'type': 'if_statement', 'children': ['131', '136', '145', '171']}; {'id': '131', 'type': 'call', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'is_empty'}; {'id': '135', 'type': 'argument_list', 'children': []}; {'id': '136', 'type': 'block', 'children': ['137', '141']}; {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'assignment', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'restriction'}; {'id': '140', 'type': 'None', 'children': []}; {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'query_string'}; {'id': '144', 'type': 'None', 'children': []}; {'id': '145', 'type': 'elif_clause', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'query_string'}; {'id': '149', 'type': 'block', 'children': ['150', '154']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}; {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'restriction'}; {'id': '153', 'type': 'None', 'children': []}; {'id': '154', 'type': 'expression_statement', 'children': ['155']}; {'id': '155', 'type': 'assignment', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'query_string'}; {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'Restriction'}; {'id': '159', 'type': 'argument_list', 'children': ['160', '161', '166']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '161', 'type': 'keyword_argument', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'folders'}; {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'folders'}; {'id': '166', 'type': 'keyword_argument', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'applies_to'}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'Restriction'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'ITEMS'}; {'id': '171', 'type': 'else_clause', 'children': ['172']}; {'id': '172', 'type': 'block', 'children': ['173', '190']}; {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'assignment', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'restriction'}; {'id': '176', 'type': 'call', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'Restriction'}; {'id': '178', 'type': 'argument_list', 'children': ['179', '180', '185']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '180', 'type': 'keyword_argument', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'folders'}; {'id': '182', 'type': 'attribute', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'folders'}; {'id': '185', 'type': 'keyword_argument', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'applies_to'}; {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'Restriction'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'ITEMS'}; {'id': '190', 'type': 'expression_statement', 'children': ['191']}; {'id': '191', 'type': 'assignment', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'query_string'}; {'id': '193', 'type': 'None', 'children': []}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}; {'id': '195', 'type': 'call', 'children': ['196', '199']}; {'id': '196', 'type': 'attribute', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '199', 'type': 'argument_list', 'children': ['200', '201', '204', '207', '208', '209', '210']}; {'id': '200', 'type': 'string', 'children': [], 'value': "'Finding %s items in folders %s (shape: %s, depth: %s, additional_fields: %s, restriction: %s)'"}; {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'folders'}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'account'}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'depth'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'additional_fields'}; {'id': '210', 'type': 'conditional_expression', 'children': ['211', '214', '215'], 'value': 'if'}; {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'restriction'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'restriction'}; {'id': '215', 'type': 'None', 'children': []}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}; {'id': '217', 'type': 'assignment', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '219', 'type': 'call', 'children': ['220', '238']}; {'id': '220', 'type': 'attribute', 'children': ['221', '237']}; {'id': '221', 'type': 'call', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'FindItem'}; {'id': '223', 'type': 'argument_list', 'children': ['224', '229', '234']}; {'id': '224', 'type': 'keyword_argument', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'account'}; {'id': '226', 'type': 'attribute', 'children': ['227', '228']}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'account'}; {'id': '229', 'type': 'keyword_argument', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'folders'}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'folders'}; {'id': '234', 'type': 'keyword_argument', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'chunk_size'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'page_size'}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'call'}; {'id': '238', 'type': 'argument_list', 'children': ['239', '242', '245', '248', '251', '254', '257', '260', '268']}; {'id': '239', 'type': 'keyword_argument', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'additional_fields'}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'additional_fields'}; {'id': '242', 'type': 'keyword_argument', 'children': ['243', '244']}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'restriction'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'restriction'}; {'id': '245', 'type': 'keyword_argument', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'order_fields'}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'order_fields'}; {'id': '248', 'type': 'keyword_argument', 'children': ['249', '250']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '251', 'type': 'keyword_argument', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'query_string'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'query_string'}; {'id': '254', 'type': 'keyword_argument', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'depth'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'depth'}; {'id': '257', 'type': 'keyword_argument', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'calendar_view'}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'calendar_view'}; {'id': '260', 'type': 'keyword_argument', 'children': ['261', '262']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'max_items'}; {'id': '262', 'type': 'conditional_expression', 'children': ['263', '266', '267'], 'value': 'if'}; {'id': '263', 'type': 'attribute', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'calendar_view'}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'max_items'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'calendar_view'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'max_items'}; {'id': '268', 'type': 'keyword_argument', 'children': ['269', '270']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '271', 'type': 'if_statement', 'children': ['272', '279', '299']}; {'id': '272', 'type': 'boolean_operator', 'children': ['273', '276'], 'value': 'and'}; {'id': '273', 'type': 'comparison_operator', 'children': ['274', '275'], 'value': '=='}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'ID_ONLY'}; {'id': '276', 'type': 'comparison_operator', 'children': ['277', '278'], 'value': 'is'}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'additional_fields'}; {'id': '278', 'type': 'None', 'children': []}; {'id': '279', 'type': 'block', 'children': ['280']}; {'id': '280', 'type': 'for_statement', 'children': ['281', '282', '283']}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '283', 'type': 'block', 'children': ['284']}; {'id': '284', 'type': 'expression_statement', 'children': ['285']}; {'id': '285', 'type': 'yield', 'children': ['286']}; {'id': '286', 'type': 'conditional_expression', 'children': ['287', '288', '293'], 'value': 'if'}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '288', 'type': 'call', 'children': ['289', '290']}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '290', 'type': 'argument_list', 'children': ['291', '292']}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '293', 'type': 'call', 'children': ['294', '297']}; {'id': '294', 'type': 'attribute', 'children': ['295', '296']}; {'id': '295', 'type': 'identifier', 'children': [], 'value': 'Item'}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'id_from_xml'}; {'id': '297', 'type': 'argument_list', 'children': ['298']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '299', 'type': 'else_clause', 'children': ['300']}; {'id': '300', 'type': 'block', 'children': ['301']}; {'id': '301', 'type': 'for_statement', 'children': ['302', '303', '304']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '304', 'type': 'block', 'children': ['305']}; {'id': '305', 'type': 'if_statement', 'children': ['306', '311', '315']}; {'id': '306', 'type': 'call', 'children': ['307', '308']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '308', 'type': 'argument_list', 'children': ['309', '310']}; {'id': '309', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '311', 'type': 'block', 'children': ['312']}; {'id': '312', 'type': 'expression_statement', 'children': ['313']}; {'id': '313', 'type': 'yield', 'children': ['314']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '315', 'type': 'else_clause', 'children': ['316']}; {'id': '316', 'type': 'block', 'children': ['317']}; {'id': '317', 'type': 'expression_statement', 'children': ['318']}; {'id': '318', 'type': 'yield', 'children': ['319']}; {'id': '319', 'type': 'call', 'children': ['320', '330']}; {'id': '320', 'type': 'attribute', 'children': ['321', '329']}; {'id': '321', 'type': 'call', 'children': ['322', '325']}; {'id': '322', 'type': 'attribute', 'children': ['323', '324']}; {'id': '323', 'type': 'identifier', 'children': [], 'value': 'Folder'}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'item_model_from_tag'}; {'id': '325', 'type': 'argument_list', 'children': ['326']}; {'id': '326', 'type': 'attribute', 'children': ['327', '328']}; {'id': '327', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '329', 'type': 'identifier', 'children': [], 'value': 'from_xml'}; {'id': '330', 'type': 'argument_list', 'children': ['331', '334']}; {'id': '331', 'type': 'keyword_argument', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'elem'}; {'id': '333', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '334', 'type': 'keyword_argument', 'children': ['335', '336']}; {'id': '335', 'type': 'identifier', 'children': [], 'value': 'account'}; {'id': '336', 'type': 'attribute', 'children': ['337', '338']}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'account'} | def find_items(self, q, shape=ID_ONLY, depth=SHALLOW, additional_fields=None, order_fields=None,
calendar_view=None, page_size=None, max_items=None, offset=0):
if shape not in SHAPE_CHOICES:
raise ValueError("'shape' %s must be one of %s" % (shape, SHAPE_CHOICES))
if depth not in ITEM_TRAVERSAL_CHOICES:
raise ValueError("'depth' %s must be one of %s" % (depth, ITEM_TRAVERSAL_CHOICES))
if not self.folders:
log.debug('Folder list is empty')
return
if additional_fields:
for f in additional_fields:
self.validate_item_field(field=f)
for f in additional_fields:
if f.field.is_complex:
raise ValueError("find_items() does not support field '%s'. Use fetch() instead" % f.field.name)
if calendar_view is not None and not isinstance(calendar_view, CalendarView):
raise ValueError("'calendar_view' %s must be a CalendarView instance" % calendar_view)
if q.is_empty():
restriction = None
query_string = None
elif q.query_string:
restriction = None
query_string = Restriction(q, folders=self.folders, applies_to=Restriction.ITEMS)
else:
restriction = Restriction(q, folders=self.folders, applies_to=Restriction.ITEMS)
query_string = None
log.debug(
'Finding %s items in folders %s (shape: %s, depth: %s, additional_fields: %s, restriction: %s)',
self.folders,
self.account,
shape,
depth,
additional_fields,
restriction.q if restriction else None,
)
items = FindItem(account=self.account, folders=self.folders, chunk_size=page_size).call(
additional_fields=additional_fields,
restriction=restriction,
order_fields=order_fields,
shape=shape,
query_string=query_string,
depth=depth,
calendar_view=calendar_view,
max_items=calendar_view.max_items if calendar_view else max_items,
offset=offset,
)
if shape == ID_ONLY and additional_fields is None:
for i in items:
yield i if isinstance(i, Exception) else Item.id_from_xml(i)
else:
for i in items:
if isinstance(i, Exception):
yield i
else:
yield Folder.item_model_from_tag(i.tag).from_xml(elem=i, account=self.account) |
Subsets and Splits