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MzIdParser.py
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MzIdParser.py
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import pyteomics.mzid as py_mzid
import re
import ntpath
import json
import sys
from time import time
from PeakListParser import PeakListParser
import zipfile
import gzip
import os
from NumpyEncoder import NumpyEncoder
class MzIdParseException(Exception):
pass
class MzIdParser:
"""
"""
def __init__(self, mzid_path, temp_dir, peak_list_dir, db, logger, db_name='', user_id=0,
origin=''):
"""
:param mzid_path: path to mzidentML file
:param temp_dir: absolute path to temp dir for unzipping/storing files
:param db: database python module to use (xiUI_pg or xiSPEC_sqlite)
:param db_name: db name for SQLite
:param origin: ftp dir of pride project
"""
self.upload_id = 0
self.mzid_path = mzid_path
self.peak_list_readers = {} # peak list readers indexed by spectraData_ref
self.temp_dir = temp_dir
if not self.temp_dir.endswith('/'):
self.temp_dir += '/'
self.peak_list_dir = peak_list_dir
if peak_list_dir and not peak_list_dir.endswith('/'):
self.peak_list_dir += '/'
self.user_id = user_id
self.random_id = 0
self.db = db
self.logger = logger
# look up table populated by parse_peptides function
# self.peptide_id_lookup = {}
self.spectra_data_protocol_map = {}
# ToDo: Might change to pyteomics unimod obo module
self.unimod_path = 'obo/unimod.obo'
# ToDo: modifications might be globally stored in mzIdentML under
# ToDo: AnalysisProtocolCollection->SpectrumIdentificationProtocol->ModificationParams
# ToDo: atm we get them while looping through the peptides
# (might be more robust and we're doing it anyway)
self.modlist = []
self.unknown_mods = []
# From mzidentML schema 1.2.0:
# <SpectrumIdentificationProtocol> must contain the CV term 'cross-linking search'
# (MS:1002494)
self.contains_crosslinks = False
self.warnings = []
# connect to DB
try:
self.con = db.connect(db_name)
self.cur = self.con.cursor()
except db.DBException as e:
self.logger.error(e)
print(e)
sys.exit(1)
self.upload_id = self.db.new_upload([user_id, os.path.basename(self.mzid_path), origin],
self.cur, self.con)
self.random_id = self.db.get_random_id(self.upload_id, self.cur, self.con)
self.upload_info_read = False
self.mzid_reader = None
def initialise_mzid_reader(self):
if self.mzid_path.endswith('.gz') or self.mzid_path.endswith('.zip'):
self.mzid_path = MzIdParser.extract_mzid(self.mzid_path)
self.logger.info('reading mzid - start ' + self.mzid_path)
start_time = time()
# schema:
# https://raw.githubusercontent.com/HUPO-PSI/mzIdentML/master/schema/mzIdentML1.2.0.xsd
try:
self.mzid_reader = py_mzid.MzIdentML(self.mzid_path)
except Exception as e:
raise MzIdParseException(type(e).__name__, e.args)
self.logger.info('reading mzid - done. Time: {} sec'.format(round(time() - start_time, 2)))
# used by TestLoop when downloading files from PRIDE
def get_supported_peak_list_file_names(self):
"""
:return: list of all supported peak list file names
"""
peak_list_file_names = []
for spectra_data_id in self.mzid_reader._offset_index["SpectraData"].keys():
sp_datum = self.mzid_reader.get_by_id(spectra_data_id, tag_id='SpectraData',
detailed=True)
ff_acc = sp_datum['FileFormat']['accession']
if any([ff_acc == 'MS:1001062', # MGF
ff_acc == 'MS:1000584', # mzML
ff_acc == 'MS:1001466', # ms2
]):
peak_list_file_names.append(ntpath.basename(sp_datum['location']))
return peak_list_file_names
# used by TestLoop when downloading files from PRIDE
def get_all_peak_list_file_names(self):
"""
:return: list of all peak list file names
"""
peak_list_file_names = []
for spectra_data_id in self.mzid_reader._offset_index["SpectraData"].keys():
sp_datum = self.mzid_reader.get_by_id(spectra_data_id, tag_id='SpectraData',
detailed=True)
peak_list_file_names.append(ntpath.basename(sp_datum['location']))
return peak_list_file_names
def init_peak_list_readers(self):
"""
sets self.peak_list_readers by looping through SpectraData elements
dictionary:
key: spectra_data_ref
value: associated peak_list_reader
"""
peak_list_readers = {}
for spectra_data_id in self.mzid_reader._offset_index["SpectraData"].keys():
sp_datum = self.mzid_reader.get_by_id(spectra_data_id, tag_id='SpectraData',
detailed=True)
self.check_spectra_data_validity(sp_datum)
sd_id = sp_datum['id']
peak_list_file_name = ntpath.basename(sp_datum['location'])
peak_list_file_path = self.peak_list_dir + peak_list_file_name
try:
peak_list_reader = PeakListParser(
peak_list_file_path,
sp_datum['FileFormat']['accession'],
sp_datum['SpectrumIDFormat']['accession']
)
except Exception:
# try gz version
try:
peak_list_reader = PeakListParser(
PeakListParser.extract_gz(peak_list_file_path + '.gz'),
sp_datum['FileFormat']['accession'],
sp_datum['SpectrumIDFormat']['accession']
)
except IOError:
raise MzIdParseException('Missing peak list file: %s' % peak_list_file_path)
peak_list_readers[sd_id] = peak_list_reader
self.peak_list_readers = peak_list_readers
def check_all_spectra_data_validity(self):
for spectra_data_id in self.mzid_reader._offset_index["SpectraData"].keys():
sp_datum = self.mzid_reader.get_by_id(spectra_data_id, tag_id='SpectraData',
detailed=True)
self.check_spectra_data_validity(sp_datum)
@staticmethod
def check_spectra_data_validity(sp_datum):
# is there anything we'd like to complain about?
# SpectrumIDFormat
if 'SpectrumIDFormat' not in sp_datum or sp_datum['SpectrumIDFormat'] is None:
raise MzIdParseException('SpectraData is missing SpectrumIdFormat')
if isinstance(sp_datum['SpectrumIDFormat'], basestring):
raise MzIdParseException('SpectraData/SpectrumIdFormat is missing accession')
if sp_datum['SpectrumIDFormat']['accession'] is None:
raise MzIdParseException('SpectraData/SpectrumIdFormat is missing accession')
# FileFormat
if 'FileFormat' not in sp_datum or sp_datum['FileFormat'] is None:
raise MzIdParseException('SpectraData is missing FileFormat')
if isinstance(sp_datum['FileFormat'], basestring):
raise MzIdParseException('SpectraData/SpectrumIdFormat is missing accession')
if sp_datum['FileFormat']['accession'] is None:
raise MzIdParseException('SpectraData/FileFormat is missing accession')
# location
if 'location' not in sp_datum or sp_datum['location'] is None:
raise MzIdParseException('SpectraData is missing location')
def parse(self):
start_time = time()
if not self.upload_info_read:
self.upload_info() # overridden (empty function) in xiSPEC subclass
if self.peak_list_dir:
self.init_peak_list_readers()
self.parse_db_sequences() # overridden (empty function) in xiSPEC subclass
self.parse_peptides()
self.parse_peptide_evidences()
self.map_spectra_data_to_protocol()
self.main_loop()
# meta_data = [self.upload_id, -1, -1, -1, -1]
# self.db.write_meta_data(meta_data, self.cur, self.con)
self.fill_in_missing_scores() # empty here, overridden in xiSPEC subclass to do stuff
self.other_info()
self.logger.info('all done! Total time: ' + str(round(time() - start_time, 2)) + " sec")
self.con.close()
def get_ion_types_mzid(self, sid_item):
try:
ion_names_list = [i['name'] for i in sid_item['IonType']]
ion_names_list = list(set(ion_names_list))
except KeyError:
return []
# ion_types = ["P"]
ion_types = []
for ion_name in ion_names_list:
try:
ion = re.search('frag: ([a-z]) ion', ion_name).groups()[0]
ion_types.append(ion)
except (IndexError, AttributeError) as e:
self.logger.info(e, ion_name)
continue
return ion_types
# split into two functions
@staticmethod
def extract_mzid(archive):
if archive.endswith('zip'):
zip_ref = zipfile.ZipFile(archive, 'r')
unzip_path = archive + '_unzip/'
zip_ref.extractall(unzip_path)
zip_ref.close()
return_file_list = []
for root, dir_names, file_names in os.walk(unzip_path):
file_names = [f for f in file_names if not f[0] == '.']
dir_names[:] = [d for d in dir_names if not d[0] == '.']
for file_name in file_names:
os.path.join(root, file_name)
if file_name.lower().endswith('.mzid'):
return_file_list.append(root+'/'+file_name)
else:
raise IOError('unsupported file type: %s' % file_name)
if len(return_file_list) > 1:
raise StandardError("more than one mzid file found!")
return return_file_list[0]
elif archive.endswith('gz'):
in_f = gzip.open(archive, 'rb')
archive = archive.replace(".gz", "")
out_f = open(archive, 'wb')
try:
out_f.write(in_f.read())
except IOError:
raise StandardError('Zip archive error: %s' % archive)
in_f.close()
out_f.close()
return archive
else:
raise StandardError('unsupported file type: %s' % archive)
def map_spectra_data_to_protocol(self):
"""
extract and map spectrumIdentificationProtocol which includes annotation data like fragment
tolerance only fragment tolerance is extracted for now
# ToDo: improve error handling
# extract modifications, cl mod mass, ...
Parameters:
------------------------
mzid_reader: pyteomics mzid_reader
"""
self.logger.info('generating spectra data protocol map - start')
start_time = time()
spectra_data_protocol_map = {}
sid_protocols = []
analysis_collection = self.mzid_reader.iterfind('AnalysisCollection').next()
for spectrumIdentification in analysis_collection['SpectrumIdentification']:
sid_protocol_ref = spectrumIdentification['spectrumIdentificationProtocol_ref']
sid_protocol = self.mzid_reader.get_by_id(sid_protocol_ref,
tag_id='SpectrumIdentificationProtocol',
detailed=True)
sid_protocols.append(sid_protocol)
try:
frag_tol = sid_protocol['FragmentTolerance']
frag_tol_plus = frag_tol['search tolerance plus value']
frag_tol_value = re.sub('[^0-9,.]', '', str(frag_tol_plus['value']))
if frag_tol_plus['unit'].lower() == 'parts per million':
frag_tol_unit = 'ppm'
elif frag_tol_plus['unit'].lower() == 'dalton':
frag_tol_unit = 'Da'
else:
frag_tol_unit = frag_tol_plus['unit']
if not all([
frag_tol['search tolerance plus value']['value'] == frag_tol['search tolerance minus value']['value'],
frag_tol['search tolerance plus value']['unit'] == frag_tol['search tolerance minus value']['unit']
]):
self.warnings.append(
{"type": "mzidParseError",
"message": "search tolerance plus value doesn't match minus value. Using plus value!"})
except KeyError:
self.warnings.append({
"type": "mzidParseError",
"message": "could not parse ms2tolerance. Falling back to default: 10 ppm.",
# 'id': id_string
})
frag_tol_value = '10'
frag_tol_unit = 'ppm'
# spectra_data_protocol_map['errors'].append(
# {"type": "mzidParseError",
# "message": "could not parse ms2tolerance. Falling back to default values."})
for inputSpectra in spectrumIdentification['InputSpectra']:
spectra_data_ref = inputSpectra['spectraData_ref']
spectra_data_protocol_map[spectra_data_ref] = {
'protocol_ref': sid_protocol_ref,
'fragmentTolerance': ' '.join([frag_tol_value, frag_tol_unit])
}
self.mzid_reader.reset()
self.spectra_data_protocol_map = spectra_data_protocol_map
self.logger.info('generating spectraData_ProtocolMap - done. Time: {} sec'.format(
round(time() - start_time, 2)))
# self.db.write.protocols()
def add_to_modlist(self, mod):
if mod['name'] == "unknown_modification":
mod['name'] = "({0:.2f})".format(mod['monoisotopicMassDelta'])
mod['monoisotopicMassDelta'] = float(mod['monoisotopicMassDelta'])
mod['residues'] = [aa for aa in mod['residues']]
if mod['name'] in [m['name'] for m in self.modlist]:
old_mod = self.modlist[[m['name'] for m in self.modlist].index(mod['name'])]
# check if modname with different mass exists already
if mod['monoisotopicMassDelta'] != old_mod['monoisotopicMassDelta']:
mod['name'] += "*"
self.add_to_modlist(mod)
else:
for res in mod['residues']:
if res not in old_mod['residues']:
old_mod['residues'].append(res)
else:
self.modlist.append(mod)
return mod['name']
def parse_db_sequences(self):
self.logger.info('parse db sequences - start')
start_time = time()
# DBSEQUENCES
inj_list = []
for db_id in self.mzid_reader._offset_index["DBSequence"].keys():
db_sequence = self.mzid_reader.get_by_id(db_id, tag_id='DBSequence', detailed=True)
data = [db_sequence["id"], db_sequence["accession"]]
# name, optional elem att
if "name" in db_sequence:
data.append(db_sequence["name"])
else :
data.append(db_sequence["accession"])
# description, officially not there?
if "protein description" in db_sequence:
data.append(json.dumps(db_sequence["protein description"], cls=NumpyEncoder))
else:
data.append(None)
# searchDatabase_ref
# Seq is optional child elem of DBSequence
if "Seq" in db_sequence and isinstance(db_sequence["Seq"], basestring):
seq = db_sequence["Seq"]
data.append(seq)
else:
# todo: get sequence
data.append("no sequence")
data.append(self.upload_id)
inj_list.append(data)
self.db.write_db_sequences(inj_list, self.cur, self.con)
self.logger.info('parse db sequences - done. Time: {} sec'.format(
round(time() - start_time, 2)))
def parse_peptides(self):
start_time = time()
self.logger.info('parse peptides, modifications - start')
# ToDo: might be stuff in pyteomics lib for this?
unimod_masses = self.get_unimod_masses(self.unimod_path)
# PEPTIDES
peptide_index = 0
peptide_inj_list = []
for pep_id in self.mzid_reader._offset_index["Peptide"].keys():
peptide = self.mzid_reader.get_by_id(pep_id, tag_id='Peptide', detailed=True)
pep_seq_dict = []
for aa in peptide['PeptideSequence']:
pep_seq_dict.append({"Modification": "", "aminoAcid": aa})
link_site = -1
crosslinker_modmass = None
value = None
# MODIFICATIONS
# add in modifications
if 'Modification' in peptide.keys():
for mod in peptide['Modification']:
if 'monoisotopicMassDelta' not in mod.keys():
try:
mod['monoisotopicMassDelta'] = unimod_masses[mod['accession']]
# ToDo: what's going on here?
except KeyError:
# seq_ref_prot_map['errors'].append({
# "type": "mzidParseError",
# "message": "could not get modification mass for modification {}".format(mod),
# "id": mod["id"]
# })
continue
# link_index = 0 # TODO: multilink support
# mod_location is 0-based for assigning modifications to correct amino acid
# mod['location'] is 1-based with 0 = n-terminal and len(pep)+1 = C-terminal
if mod['location'] == 0:
mod_location = 0
# n_terminal_mod = True
elif mod['location'] == len(peptide['PeptideSequence']) + 1:
mod_location = mod['location'] - 2
# c_terminal_mod = True
else:
mod_location = mod['location'] - 1
# n_terminal_mod = False
# c_terminal_mod = False
if 'residues' not in mod:
mod['residues'] = peptide['PeptideSequence'][mod_location]
# TODO - issues here with using names rather than cv param accession
# (cross-link acceptor/ receiver)
if 'name' in mod.keys():
# fix mod names
if isinstance(mod['name'], list): # todo: have a look at this - cc
mod['name'] = ','.join(mod['name'])
mod['name'] = mod['name'].lower()
mod['name'] = mod['name'].replace(" ", "_")
if 'cross-link donor' not in mod.keys() and 'cross-link acceptor' not in mod.keys() and 'cross-link receiver' not in mod.keys():
cur_mod = pep_seq_dict[mod_location]
# join modifications into one for multiple modifications on the same aa
if not cur_mod['Modification'] == '':
mod['name'] = '_'.join(sorted([cur_mod['Modification'], mod['name']], key=str.lower))
cur_mod_mass = [x['monoisotopicMassDelta'] for x in self.modlist if x['name'] == cur_mod['Modification']][0]
mod['monoisotopicMassDelta'] += cur_mod_mass
# save to all mods list and get back new_name
mod['name'] = self.add_to_modlist(mod)
cur_mod['Modification'] = mod['name']
# error handling for mod without name
else:
# cross-link acceptor doesn't have a name
if 'cross-link acceptor' not in mod.keys() and 'cross-link receiver' not in mod.keys():
raise MzIdParseException("Missing modification name")
# add CL locations
if 'cross-link donor' in mod.keys() or 'cross-link acceptor' in mod.keys()\
or 'cross-link receiver' in mod.keys():
# use mod['location'] for link-site (1-based in database in line with mzIdentML specifications)
link_site = mod['location']
crosslinker_modmass = mod['monoisotopicMassDelta']
if 'cross-link acceptor' in mod.keys():
value = mod['cross-link acceptor']['value']
if 'cross-link donor' in mod.keys():
value = mod['cross-link donor']['value']
if 'cross-link receiver' in mod.keys():
value = mod['cross-link receiver']['value']
# ToDo: we should consider swapping these over because modX format has modification
# before AA
peptide_seq_with_mods = ''.join(
[''.join([x['aminoAcid'], x['Modification']]) for x in pep_seq_dict])
data = [
# peptide_index, # debug use mzid peptide['id'],
peptide['id'],
peptide_seq_with_mods,
link_site,
crosslinker_modmass,
self.upload_id,
str(value)
]
peptide_inj_list.append(data)
# self.peptide_id_lookup[peptide['id']] = peptide_index
if peptide_index % 1000 == 0:
self.logger.info('writing 1000 peptides to DB')
try:
self.db.write_peptides(peptide_inj_list, self.cur, self.con)
peptide_inj_list = []
self.con.commit()
except Exception as e:
raise e
peptide_index += 1
try:
self.db.write_peptides(peptide_inj_list, self.cur, self.con)
self.con.commit()
except Exception as e:
raise e
#
mod_index = 0
modifications_inj_list = []
for mod in self.modlist:
try:
mod_accession = mod['accession']
except KeyError:
mod_accession = ''
modifications_inj_list.append([
mod_index,
self.upload_id,
mod['name'],
mod['monoisotopicMassDelta'],
''.join(mod['residues']),
mod_accession
])
mod_index += 1
self.db.write_modifications(modifications_inj_list, self.cur, self.con)
self.logger.info('parse peptides, modifications - done. Time: {} sec'.format(
round(time() - start_time, 2)))
def parse_peptide_evidences(self):
start_time = time()
self.logger.info('parse peptide evidences - start')
seq_id_to_acc_map = {}
for db_id in self.mzid_reader._offset_index["DBSequence"].keys():
db_sequence = self.mzid_reader.get_by_id(db_id, tag_id='DBSequence', detailed=True)
seq_id_to_acc_map[db_sequence["id"]] = db_sequence["accession"]
# PEPTIDE EVIDENCES
inj_list = []
for pep_ev_id in self.mzid_reader._offset_index["PeptideEvidence"].keys():
peptide_evidence = self.mzid_reader.get_by_id(pep_ev_id, tag_id='PeptideEvidence',
detailed=True)
pep_start = -1
if "start" in peptide_evidence:
pep_start = peptide_evidence["start"] # start att, optional
is_decoy = False
if "isDecoy" in peptide_evidence:
is_decoy = peptide_evidence["isDecoy"] # isDecoy att, optional
# peptide_ref = self.peptide_id_lookup[peptide_evidence["peptide_ref"]]
peptide_ref = peptide_evidence["peptide_ref"] # debug use mzid peptide['id'],
data = [
peptide_ref, # 'peptide_ref',
peptide_evidence["dBSequence_ref"], # 'dbsequence_ref',
seq_id_to_acc_map[peptide_evidence["dBSequence_ref"]], # 'protein_accession',
pep_start, # 'pep_start',
is_decoy, # 'is_decoy',
self.upload_id # 'upload_id'
]
inj_list.append(data)
if len(inj_list) % 1000 == 0:
self.logger.info('writing 1000 peptide_evidences to DB')
try:
self.db.write_peptide_evidences(inj_list, self.cur, self.con)
inj_list = []
self.con.commit()
except Exception as e:
raise e
try:
self.db.write_peptide_evidences(inj_list, self.cur, self.con)
self.con.commit()
except Exception as e:
raise e
self.con.commit()
self.mzid_reader.reset()
self.logger.info('parse peptide evidences - done. Time: {} sec'.format(
round(time() - start_time, 2)))
@staticmethod
def get_unimod_masses(unimod_path):
masses = {}
mod_id = -1
with open(unimod_path) as f:
for line in f:
if line.startswith('id: '):
mod_id = ''.join(line.replace('id: ', '').split())
elif line.startswith('xref: delta_mono_mass ') and not mod_id == -1:
mass = float(line.replace('xref: delta_mono_mass ', '').replace('"', ''))
masses[mod_id] = mass
return masses
def main_loop(self):
spec_id = 0
identification_id = 0
spectra = []
spectrum_identifications = []
fragment_parsing_error_scans = []
#
# main loop
main_loop_start_time = time()
self.logger.info('main loop - start')
for sid_result in self.mzid_reader:
if self.peak_list_dir:
peak_list_reader = self.peak_list_readers[sid_result['spectraData_ref']]
scan_id = peak_list_reader.parse_scan_id(sid_result["spectrumID"])
scan = peak_list_reader.get_scan(scan_id)
protocol = self.spectra_data_protocol_map[sid_result['spectraData_ref']]
if scan['precursor'] is not None:
precursor_mz = scan['precursor']['mz']
precursor_charge = scan['precursor']['charge']
else:
# give warning precursor info is missing
precursor_mz = None
precursor_charge = None
spectra.append([
spec_id,
scan['peaks'],
ntpath.basename(peak_list_reader.peak_list_path),
str(scan_id),
protocol['fragmentTolerance'],
self.upload_id,
sid_result['id'],
precursor_mz,
precursor_charge
])
spectrum_ident_dict = dict()
linear_index = -1 # negative index values for linear peptides
for spec_id_item in sid_result['SpectrumIdentificationItem']:
# get suitable id
if 'cross-link spectrum identification item' in spec_id_item.keys():
self.contains_crosslinks = True
cross_link_id = spec_id_item['cross-link spectrum identification item']
else: # assuming linear
# misusing 'cross-link spectrum identification item'
# for linear peptides with negative index
# specIdItem['cross-link spectrum identification item'] = linear_index
# spec_id_set.add(get_cross_link_identifier(specIdItem))
cross_link_id = linear_index
linear_index -= 1
# check if seen it before
if cross_link_id in spectrum_ident_dict.keys():
# do crosslink specific stuff
ident_data = spectrum_ident_dict.get(cross_link_id)
# ident_data[4] = self.peptide_id_lookup[spec_id_item['peptide_ref']]
ident_data[4] = spec_id_item['peptide_ref'] # debug
else:
# do stuff common to linears and crosslinks
charge_state = spec_id_item['chargeState']
pass_threshold = spec_id_item['passThreshold']
# ToDo: refactor with MS: cv Param list of all scores
scores = {
k: v for k, v in spec_id_item.iteritems()
if 'score' in k.lower() or
'pvalue' in k.lower() or
'evalue' in k.lower() or
'sequest' in k.lower() or
'scaffold' in k.lower()
}
#
# fragmentation ions
# ToDo: do we want to make assumptions of fragIon types by fragMethod from mzML?
ions = self.get_ion_types_mzid(spec_id_item)
# if no ion types are specified in the id file check the mzML file
# if len(ions) == 0 and peak_list_reader['fileType'] == 'mzml':
# ions = peakListParser.get_ion_types_mzml(scan)
ions = list(set(ions))
if len(ions) == 0:
ions = ['peptide', 'b', 'y']
# ToDo: better error handling for general errors -
# bundling together of same type errors
fragment_parsing_error_scans.append(sid_result['id'])
ions = ';'.join(ions)
# extract other useful info to display
rank = spec_id_item['rank']
# from mzidentML schema 1.2.0: For PMF data, the rank attribute may be
# meaningless and values of rank = 0 should be given.
# xiSPEC front-end expects rank = 1 as default
if rank is None or int(rank) == 0:
rank = 1
experimental_mass_to_charge = spec_id_item['experimentalMassToCharge']
try:
calculated_mass_to_charge = spec_id_item['calculatedMassToCharge']
except KeyError:
calculated_mass_to_charge = None
ident_data = [
identification_id,
# spec_id_item['id'],
self.upload_id,
spec_id,
# self.peptide_id_lookup[spec_id_item['peptide_ref']], # debug use spec_id_item['peptide_ref'],
spec_id_item['peptide_ref'],
'', # pep2
charge_state,
rank,
pass_threshold,
ions,
json.dumps(scores),
experimental_mass_to_charge,
calculated_mass_to_charge,
"",
"",
""
]
spectrum_ident_dict[cross_link_id] = ident_data
identification_id += 1
spectrum_identifications += spectrum_ident_dict.values()
spec_id += 1
if spec_id % 1000 == 0:
self.logger.info('writing 1000 entries (1000 spectra and their idents) to DB')
try:
self.db.write_spectra(spectra, self.cur, self.con)
spectra = []
self.db.write_spectrum_identifications(spectrum_identifications, self.cur,
self.con)
spectrum_identifications = []
self.con.commit()
except Exception as e:
raise e
# end main loop
self.logger.info('main loop - done Time: {} sec'.format(
round(time() - main_loop_start_time, 2)))
# once loop is done write remaining data to DB
db_wrap_up_start_time = time()
self.logger.info('write remaining entries to DB - start')
try:
self.db.write_spectra(spectra, self.cur, self.con)
self.db.write_spectrum_identifications(spectrum_identifications, self.cur, self.con)
self.con.commit()
except Exception as e:
raise e
self.logger.info('write remaining entries to DB - start - done. Time: {} sec'.format(
round(time() - db_wrap_up_start_time, 2)))
self.ident_count = identification_id
# warnings
if len(fragment_parsing_error_scans) > 0:
if len(fragment_parsing_error_scans) > 50:
id_string = '; '.join(fragment_parsing_error_scans[:50]) + ' ...'
else:
id_string = '; '.join(fragment_parsing_error_scans)
self.warnings.append({
"type": "IonParsing",
"message": "mzidentML file does not specify fragment ions.",
'id': id_string
})
def upload_info(self):
self.upload_info_read = True
upload_info_start_time = time()
self.logger.info('parse upload info - start')
peak_list_file_names = json.dumps(self.get_all_peak_list_file_names(), cls=NumpyEncoder)
spectra_formats = []
for spectra_data_id in self.mzid_reader._offset_index["SpectraData"].keys():
sp_datum = self.mzid_reader.get_by_id(spectra_data_id, tag_id='SpectraData',
detailed=True)
spectra_formats.append(sp_datum)
spectra_formats = json.dumps(spectra_formats, cls=NumpyEncoder)
# AnalysisSoftwareList - optional element
# see https://groups.google.com/forum/#!topic/pyteomics/Mw4eUHmicyU
self.mzid_reader.schema_info['lists'].add("AnalysisSoftware")
try:
analysis_software = json.dumps(self.mzid_reader.iterfind('AnalysisSoftwareList').next()['AnalysisSoftware'])
except StopIteration:
analysis_software = '{}'
except Exception as e:
raise MzIdParseException(type(e).__name__, e.args)
self.mzid_reader.reset()
# Provider - optional element
try:
provider = json.dumps(self.mzid_reader.iterfind('Provider').next())
except StopIteration:
provider = '{}'
except Exception as e:
raise MzIdParseException(type(e).__name__, e.args)
self.mzid_reader.reset()
# AuditCollection - optional element
audits = '{}'
try:
audits = json.dumps(self.mzid_reader.iterfind('AuditCollection').next())
except StopIteration:
audits = '{}'
except Exception as e:
raise MzIdParseException(type(e).__name__, e.args)
self.mzid_reader.reset()
# AnalysisSampleCollection - optional element
try:
samples = json.dumps(self.mzid_reader.iterfind('AnalysisSampleCollection').next()['Sample'])
except StopIteration:
samples = '{}'
except Exception as e:
raise MzIdParseException(type(e).__name__, e.args)
self.mzid_reader.reset()
# AnalysisCollection - required element, StopIteration exception shouldn't happen
try:
analyses = json.dumps(self.mzid_reader.iterfind('AnalysisCollection').next()['SpectrumIdentification'])
except StopIteration:
analyses = '{}' # could legitimately throw error here instead, its required
except Exception as e:
raise MzIdParseException(type(e).__name__, e.args)
self.mzid_reader.reset()
# AnalysisProtocolCollection - required element
try:
protocol_collection = self.mzid_reader.iterfind('AnalysisProtocolCollection').next()
protocols = json.dumps(protocol_collection['SpectrumIdentificationProtocol'],
cls=NumpyEncoder)
except StopIteration:
protocols = '{}' # could legitimately throw error here instead, its required
except Exception as e:
raise MzIdParseException(type(e).__name__, e.args)
self.mzid_reader.reset()
# BibliographicReference - optional element
bibRefs = []
for bib in self.mzid_reader.iterfind('BibliographicReference'):
bibRefs.append(bib)
bibRefs = json.dumps(bibRefs)
self.mzid_reader.reset()
self.db.write_mzid_info(peak_list_file_names,
spectra_formats,
analysis_software,
provider,
audits,
samples,
analyses,
protocols,
bibRefs,
self.upload_id, self.cur, self.con)
self.logger.info('getting upload info - done Time: {} sec'.format(
round(time() - upload_info_start_time, 2)))
def fill_in_missing_scores(self):
pass
def other_info(self):
ident_file_size = os.path.getsize(self.mzid_path)
self.db.write_other_info(self.upload_id, self.contains_crosslinks, self.ident_count,
ident_file_size, self.warnings, self.cur, self.con)
class xiSPEC_MzIdParser(MzIdParser):
def upload_info(self):
pass
def parse_db_sequences(self):
pass
def fill_in_missing_scores(self):
# Fill missing scores with
score_fill_start_time = time()
self.logger.info('fill in missing scores - start')
self.db.fill_in_missing_scores(self.cur, self.con)
self.logger.info('fill in missing scores - done. Time: {}'.format(
round(time() - score_fill_start_time, 2)))
def other_info(self):
pass