for isotopelabel_id, data in allsumionratiodata.iteritems():
allfractionbgratios[isotopelabel_id] = np.median(data)
# second normalization so that the bg-ratios all add to 1
for isotopelabel_id, data in allfractionbgratios.iteritems():
allfractionbgratios[isotopelabel_id] = data / sum(allfractionbgratios.values())
logger.log.debug(('allfractionbgratios are %s' % str(allfractionbgratios)))
for corrects2iquantob in corrects2iquantoblist:
# perform correction for each of the analyzed .hdf5 files.
s2icorrecteddata = corrects2iquantob.performS2Icorrection(allfractionbgratios)
corrects2iquantob.hdf5corrects2iquant.updates2ivalues(s2icorrecteddata)
hdf5corrects2iquant.close()
except ExHa.czException as czEx:
ExHa.reformatException(czEx)
ExHa.addContext(czEx, 'Error during corrects2iquant run')
ExHa.exportError2File(czEx, cfg.parameters['runtime']['datadir'] / Path('errors.error'))
if logger:
logger.log.warning(ExHa.oneLineRepr(czEx))
else:
print ExHa.multiLineRepr(czEx)
except Exception as genEx:
ExHa.reformatException(genEx)
ExHa.addContext(genEx, 'Error during corrects2iquant run')
ExHa.exportError2File(genEx, cfg.parameters['runtime']['datadir'] / 'errors.error')
if logger:
logger.log.warning(ExHa.oneLineRepr(genEx))
else:
print ExHa.multiLineRepr(genEx)
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()
jobcontrol(cfg, logger)
except ExHa.UsageError as useEx:
ExHa.reformatException(useEx)
print useEx.context
except Exception as genEx:
ExHa.reformatException(genEx)
errorFile = Path(cfg.parameters['runtime']['hdf5file']).stem + '.error'
ExHa.exportError2File(
genEx, cfg.parameters['runtime']['datadir'].joinpath(errorFile))
if logs:
logs.datlog.warning(ExHa.oneLineRepr(genEx))
else:
print ExHa.multiLineRepr(genEx)
importer.importData.mascot_matched_spectra)
logger.log.info('Total Spectra Matched = %6i' %
importer.importData.spectra_in_qc_proteins)
logger.log.info('Total Spectra w Quant = %6i' %
importer.importData.quantified_spectra)
logger.log.info('Total Spectra All Rep = %6i' %
importer.importData.numSpectraAllReporters)
times = sw.stop()
logger.log.info(sw.format())
hdf5results.close()
except ExHa.UsageError as useEx:
ExHa.reformatException(useEx)
logger.log.warning(ExHa.oneLineRepr(useEx))
except Exception as genEx:
# error
if logger:
logger.log.warning(ExHa.oneLineRepr(genEx))
print ExHa.multiLineRepr(genEx)
else:
print ExHa.multiLineRepr(genEx)
if cfg:
ExHa.exportError2File(genEx,
dataDir.joinpath(resultfile.stem + '.error'))
else:
ExHa.exportError2File(genEx, dataDir.joinpath('errors.error'))
sys.exit(ExHa.oneLineRepr(genEx))
for f in dataDir.glob(fileFilter):
if not f.is_file():
# skip any directories
continue
# if f.name[:4] in ['6528', '1814', '2032']: continue
mgf = mgftools(f)
logger.log.info('Filename: %s' % f.name)
if hcdOnly:
logger.log.info('Export HCD data only')
else:
logger.log.info('Using filters: %s' % str(mgf.usefilts))
rtn = mgf.export(hcdOnly)
mgf.close()
if f == 0:
raise ExHa.MGFprocessingError('no files found for: %s' %
str(dataDir / fileFilter))
except ExHa.UsageError as useEx:
ExHa.reformatException(useEx)
logger.log.info(useEx.context)
except Exception, genEx:
ExHa.reformatException(genEx)
if f:
ExHa.exportError2File(genEx, f.parent.joinpath(f.stem + '.error'))
else:
ExHa.exportError2File(genEx, dataDir.joinpath('errors.error'))
logger.log.info(ExHa.multiLineRepr(genEx))
logger.log.info('finished')
from CommonUtils.LoggingManager import Logger
from CommonUtils.hdf5Base import hdf5Base
from CommonUtils.QuantMethodHandler import QuantMethods
import CommonUtils.ExceptionHandler as ExHa
# pyMSsafe modules
try:
from xRawFile import XRawFile
except ImportError, ieEx:
ExHa.reformatException(ieEx)
ExHa.addContext(ieEx, 'Xcalibur not set up properly')
configPath = './pymssafe.cfg'
cfg = pyMSsafeConfigManager(configPath)
ret = cfg.evaluateCommandLineArgs(sys.argv)
dataDir = cfg.parameters['runtime']['datadir']
ExHa.exportError2File(ieEx, dataDir.joinpath('errors.error'))
from datastore import Datamanager
class pymssafe:
def __init__(self, config):
"""
@brief initiaise pyMSsafe controller
@param mode <string>: operational mode of the application
"""
self.cfg = config
dataDir = cfg.parameters['runtime']['datadir']
logParam = cfg.parameters['logging']
