def runProteinInference(fileList):
fileListString = ','.join(fileList)
timeString = time.strftime('%Y%m%d_%H%M', time.localtime(time.time()))
suffix = 'results_%s.hdf5' % timeString
if len(fileList) > 1:
infoStr = 'Starting merged protein inference for %i files'
resultFile = '%s_merged_%s' % (dataDir.name[:25], suffix)
logger.log.log(logger.PROCESS, infoStr % len(fileList))
else:
infoStr = 'Starting protein inference for %s'
resultFile = '%s_%s_%s' % (dataDir.name[:25], Path(fileList[0]).stem, suffix)
logger.log.log(logger.PROCESS, infoStr % fileListString)
cwd = os.getcwd()
os.chdir('proteinInference')
general = cfg.parameters['general']
cmdline = 'python proteinInference.py --datadir %s --filelist %s --resultfilename %s' + logFormat
cmdline += ' --general.fdrthreshold %s '
cmdline = cmdline % (str(dataDir), fileListString, resultFile, cfg.parameters['logging']['logdir'],
cfg.parameters['logging']['loglevel'], cfg.parameters['logging']['screenlevel'],
general['fdrthreshold'])
if quantMeth:
cmdline += ' --quantmethod_id %s' % quantMeth['meth_id']
else:
cmdline += ' --quantmethod_id none'
logger.log.debug('cmd: %s' % cmdline)
os.system(cmdline)
resultPath = dataDir.joinpath(resultFile)
ret = fetchError(dataDir.joinpath(resultPath.stem + '.error'))
ret['resultfile'] = resultPath
ret['suffix'] = suffix
ret['cmdline'] = cmdline
if ret['code'] == 0:
# add in the parameters from pymssafe if successfully ran protein inference
os.chdir(cwd)
preCfg = ConfigManager(Path('./preMascot.cfg'))
hdf = HDF5Results(resultPath)
hdf.appendOpen()
hdf.addConfigParameters(preCfg.parameters, 'preMascot', '1 pyMSsafe')
hdf.close()
ret = fetchError(dataDir.joinpath(resultPath.stem + '.error'))
ret['resultfile'] = resultPath
ret['suffix'] = suffix
ret['cmdline'] = cmdline
os.chdir(cwd)
return ret
def __init__(self):
modulePath = Path(__file__).parent
for pth in modulePath.parents:
configPath = pth.joinpath('QuantMethod.cfg')
if configPath.exists():
break
cfg = ConfigManager(str(configPath))
self.methodsByName = {}
self.methodsByID = {}
for s in cfg.parameters:
meth = cfg.parameters[s]
method = {'quantmasses': {}}
for key in meth:
if key in ['__name__']:
continue
elif key in ['meth_id', 'batch_id', 'num_isotopes']:
method[key] = int(meth[key])
elif key in ['heavy_isotopes']:
method[key] = eval(meth[key])
elif key in ['hyperplexed', 'xic_only']:
if meth[key].lower(
) == 'yes' or meth[key] == '1' or meth[key] == 'True':
method[key] = True
else:
method[key] = False
else:
try:
iso = int(key)
method['quantmasses'][iso] = eval(meth[key])
except ValueError:
method[key] = meth[key]
self.methodsByID[method['meth_id']] = copy.deepcopy(method)
self.methodsByName[method['meth_name'].upper()] = copy.deepcopy(
method)
mys2icorrecteddata[spectrum_id][isotopelabel_id] = s2icorr
else:
self.cfg.log.debug('no spectrum_id (%s) for s2i correction ' % spectrum_id)
for isotopelabel_id, val in data.iteritems():
if spectrum_id not in mys2icorrecteddata:
mys2icorrecteddata[spectrum_id] = {}
mys2icorrecteddata[spectrum_id][isotopelabel_id] = val
pBar.finish()
self.s2icorrecteddata = mys2icorrecteddata
self.cfg.log.info('done performS2Icorrection')
return mys2icorrecteddata
if __name__ == "__main__":
logger = 0
cfg = ConfigManager('./corrects2iquant.cfg')
try:
configErr = cfg.evaluateCommandLineArgs(sys.argv)
dataDir = cfg.parameters['runtime']['datadir']
# start the logging process
logParam = cfg.parameters['logging']
logPath = Path(dataDir.joinpath(logParam['logdir']))
if not logPath.exists():
logPath.mkdir(parents=True)
logFile = logPath.joinpath(logParam['logfile'])
logger = Logger(logFile, logParam['loglevel'], logParam['screenlevel'], False)
logger.setLog('corrects2iquant')
cfg.log = logger.log
hdf5files = [Path(cfg.parameters['runtime']['datadir'], cfg.parameters['runtime']['filename'])]
allpeptideratios = {}
finally:
hdfMascot.close()
logs.setuplog.info('Closing HDF5')
hdfMascot.close()
watch.rec('processing')
watch.stop()
logs.setuplog.info('job took %s' % watch.format())
return
# ########### MAIN ###############
if __name__ == '__main__':
logs = 0
# try:
cfg = ConfigManager('./mascotparser.cfg')
ret = cfg.evaluateCommandLineArgs(sys.argv)
try:
cfg.scalePpmMda()
dataDir = cfg.parameters['runtime']['datadir']
logParam = cfg.parameters['logging']
logPath = Path(dataDir.joinpath(logParam['logdir']))
if not logPath.exists():
logPath.mkdir(parents=True)
logFile = logPath.joinpath(logParam['logfile'])
logger = Logger(logFile, logParam['loglevel'], logParam['screenlevel'],
False)
logger.setMascotParserLogs()
else:
# provide command line for pyMSsafe scripts
argStr = '--datadir %s --filefilter %s* --pid %i --quant %s --general.tolppm %s --general.tolmda %s '
argStr += '--xic.beforepeak %s --xic.afterpeak %s' + logStr
argStr = argStr % (direc, file, pID, cfg.parameters['runtime']['quant'], general['tolppm'], general['tolmda'],
general['beforepeak'], general['afterpeak'])
return argStr
if __name__ == '__main__':
sysPlatform = sys.platform
if sysPlatform != 'win32':
raise OSError('Invalid operating system (%s) for running analysis, "win32" needed.' % sysPlatform)
configPath = './preMascot.cfg'
cfg = ConfigManager(configPath)
ret = cfg.evaluateCommandLineArgs(sys.argv)
pID = os.getpid()
# instrument = cfg.parameters['runtime']['instrument']
dataDir = cfg.parameters['runtime']['datadir']
pyMSsafeAppDir = str(Path('./pyMSsafe').resolve())
logParam = cfg.parameters['logging']
logPath = Path(dataDir.joinpath(logParam['logdir']))
if logPath.exists():
# clear existing logs for this part of the pipeline
for log in logPath.glob('*.log'):
if log.name in ['preMascot.log', 'pyMSsafe.log', 'mgfCreation.log']:
log.unlink()
in_quantification_of_protein=0,
fdr_at_score=fdr_at_score)
quantList.append(specQuantDict.copy())
deltas.append(q['mzdiff'])
return quantList, deltas
if __name__ == '__main__':
logger = None
cfg = None
installdir = Path(os.path.dirname(__file__))
confile = installdir / Path('proteininference.cfg')
cfg = ConfigManager(str(confile))
ret = cfg.evaluateCommandLineArgs(sys.argv)
searches = sorted(cfg.parameters['runtime']['filelist'])
dataDir = cfg.parameters['runtime']['datadir']
resultfile = dataDir.joinpath(cfg.parameters['runtime']['resultfilename'])
try:
# start the logging process
logParam = cfg.parameters['logging']
logPath = Path(dataDir.joinpath(logParam['logdir']))
if not logPath.exists():
logPath.mkdir(parents=True)
logFile = logPath.joinpath(logParam['logfile'])
logger = Logger(logFile, logParam['loglevel'], logParam['screenlevel'],
True)
dict(protein_group_no=protein_group_no,
isotopelabel_id=isotopelabel_id,
reference_label=str(reference),
protein_fold_change=protein_fold_change,
lower_confidence_level=lower_confidence_level,
upper_confidence_level=upper_confidence_level,
sum_quant_signal=sumdata,
qssm=qssm,
qupm=qupm))
self.hdf5quantprot.writeProteinQuant(prepareddata)
if __name__ == "__main__":
logger = 0
cfg = ConfigManager('./proteinquantification.cfg')
try:
configErr = cfg.evaluateCommandLineArgs(sys.argv)
dataDir = cfg.parameters['runtime']['datadir']
# start the logging process
logParam = cfg.parameters['logging']
logPath = Path(dataDir.joinpath(logParam['logdir']))
if not logPath.exists():
logPath.mkdir(parents=True)
logFile = logPath.joinpath(logParam['logfile'])
logger = Logger(logFile, logParam['loglevel'], logParam['screenlevel'],
False)
logger.setLog('proteinQuantification')
cfg.log = logger.log