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1b166bd
1
Parent(s):
9058c14
Update code/pdb_featureVector.py
Browse files
code/pdb_featureVector.py
CHANGED
@@ -40,9 +40,9 @@ from add_alignment import *
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from manage_files import *
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from add_3Dalignment import *
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from add_sasa import *
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from standard import
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from standard import finalTouch
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from add_interface_pos import *
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from utils import *
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from pdbMapping import *
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from uniprotSequenceMatch import uniprotSequenceMatch
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@@ -309,7 +309,6 @@ def pdb(input_set, mode, impute):
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print('Extracting interface residues...\n')
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data_interface = pd.read_csv(path_to_interfaces, sep='\t')
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-
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positions = get_interface_positions(data_interface, 'P1', 'P2')
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@@ -318,15 +317,10 @@ def pdb(input_set, mode, impute):
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for key, val in positions.items():
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k = pd.Series((key, str(list(set(val)))))
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interface_dataframe = interface_dataframe.append(k, ignore_index=True)
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interface_dataframe.columns = ['uniprotID', 'positions']
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st.write('HERE')
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data = finalTouch(allData)
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st.write('finalTouch')
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st.write(data.head())
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data = data.merge(interface_dataframe, on='uniprotID', how='left')
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data.positions = data.positions.astype('str')
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st.write('passed')
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for i in data.index:
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if (str(data.at[i, 'pos']) in data.at[i, 'positions']) and data.at[i, 'trsh4'] == 'surface':
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data.at[i, 'threeState_trsh4_HQ'] = 'interface'
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@@ -465,4 +459,6 @@ def pdb(input_set, mode, impute):
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minutes, seconds = divmod(rem, 60)
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print("Time passed: {:0>2}:{:0>2}:{:05.2f}".format(int(hours), int(minutes), seconds))
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#sys.stdout.close()
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return data
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from manage_files import *
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from add_3Dalignment import *
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from add_sasa import *
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from standard import *
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from add_interface_pos import *
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from standard import *
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from utils import *
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from pdbMapping import *
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from uniprotSequenceMatch import uniprotSequenceMatch
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print('Extracting interface residues...\n')
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data_interface = pd.read_csv(path_to_interfaces, sep='\t')
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positions = get_interface_positions(data_interface, 'P1', 'P2')
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for key, val in positions.items():
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k = pd.Series((key, str(list(set(val)))))
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interface_dataframe = interface_dataframe.append(k, ignore_index=True)
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interface_dataframe.columns = ['uniprotID', 'positions']
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data = finalTouch(allData)
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data = data.merge(interface_dataframe, on='uniprotID', how='left')
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data.positions = data.positions.astype('str')
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for i in data.index:
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if (str(data.at[i, 'pos']) in data.at[i, 'positions']) and data.at[i, 'trsh4'] == 'surface':
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data.at[i, 'threeState_trsh4_HQ'] = 'interface'
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minutes, seconds = divmod(rem, 60)
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print("Time passed: {:0>2}:{:0>2}:{:05.2f}".format(int(hours), int(minutes), seconds))
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#sys.stdout.close()
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return data
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