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comments = re.findall('""([^""]*)""', line)
for c in comments:
self._parse_meta_info(c)
self._parse_compound_info(c)
####################################################
# parse meta and compound info lines
####################################################
# check the current line for both general meta data
# and compound information
self._parse_meta_info(line)
self._parse_compound_info(line)
####################################################
# End of meta data
####################################################
# Most MSP files have the a standard line of text before the spectra information begins. Here we check
# for this line and store the relevant details for the compound and meta information to be ready for insertion
# into the database
if self.collect_meta and (re.match('^Num Peaks(.*)$', line, re.IGNORECASE) or re.match('^PK\$PEAK:(.*)', line,
re.IGNORECASE) or re.match('^PK\$ANNOTATION(.*)', line, re.IGNORECASE)):
self._store_compound_info()
self._store_meta_info()
# Reset the temp meta and compound information
self.meta_info = get_blank_dict(self.meta_regex)
self.compound_info = get_blank_dict(self.compound_regex)
self.other_names = []
self.collect_meta = False
# ignore additional information in the 3rd column if using the MassBank spectra schema
if re.match('^PK\$PEAK: m/z int\. rel\.int\.$', line, re.IGNORECASE):
self.ignore_additional_spectra_info = True
# Check if annnotation or spectra is to be in the next lines to be parsed
if re.match('^Num Peaks(.*)$', line, re.IGNORECASE) or re.match('^PK\$PEAK:(.*)', line, re.IGNORECASE):
self.start_spectra = True
return
elif re.match('^PK\$ANNOTATION(.*)', line, re.IGNORECASE):
self.start_spectra_annotation = True
match = re.match('^PK\$ANNOTATION:(.*)', line, re.IGNORECASE)
columns = match.group(1)
cl = columns.split()
self.spectra_annotation_indexes = {i: cl.index(i) for i in cl}
return
####################################################
# Process annotation details
####################################################
# e.g. molecular formula for each peak in the spectra
if self.start_spectra_annotation:
self._parse_spectra_annotation(line)
####################################################
# Process spectra
####################################################
if self.start_spectra:
self._parse_spectra(line)"
159,"def get_compound_ids(self):
""""""Extract the current compound ids in the database. Updates the self.compound_ids list
""""""
cursor = self.conn.cursor()
cursor.execute('SELECT inchikey_id FROM metab_compound')
self.conn.commit()
for row in cursor:
if not row[0] in self.compound_ids:
self.compound_ids.append(row[0])"
160,"def _store_compound_info(self):
""""""Update the compound_info dictionary with the current chunk of compound details
Note that we use the inchikey as unique identifier. If we can't find an appropiate inchikey we just use
a random string (uuid4) suffixed with UNKNOWN
""""""
other_name_l = [name for name in self.other_names if name != self.compound_info['name']]
self.compound_info['other_names'] = ' <#> '.join(other_name_l)
if not self.compound_info['inchikey_id']:
self._set_inchi_pcc(self.compound_info['pubchem_id'], 'cid', 0)
if not self.compound_info['inchikey_id']:
self._set_inchi_pcc(self.compound_info['smiles'], 'smiles', 0)
if not self.compound_info['inchikey_id']:
self._set_inchi_pcc(self.compound_info['name'], 'name', 0)
if not self.compound_info['inchikey_id']:
print('WARNING, cant get inchi key for ', self.compound_info)
print(self.meta_info)
print('#########################')
self.compound_info['inchikey_id'] = 'UNKNOWN_' + str(uuid.uuid4())
if not self.compound_info['pubchem_id'] and self.compound_info['inchikey_id']:
self._set_inchi_pcc(self.compound_info['inchikey_id'], 'inchikey', 0)
if not self.compound_info['name']:
self.compound_info['name'] = 'unknown name'