allfractionbgratios = {}
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:
class mgftools:
def __init__(self, hdf5file):
"""
@brief initialises the mgftools class
@param hdf5file <string/path>: path for the hdf5 file to analyse
"""
self.cfgFilters = cfg.parameters['msmsfilters']
self.maxint = 0
self.proton = cfg.parameters['general']['proton']
self.neutron = cfg.parameters['general']['neutron']
self.hdf5 = hdf5Base(hdf5file)
self.hdf5.readOpen()
self.filters = dict(ten=self.tenpercent,
zone=self.zonefilter,
repion=self.repionfilter,
deconv=self.deconvolute,
mascot=self.mascot,
neutralloss=self.neutrallossfilter,
multi=self.multichargefilt,
immonium=self.immoniumfilter,
none='')
self.isos = self.hdf5.readTable('/rawdata/isotopes')
frags = self.getActivationTypes()
if len(frags) == 1:
if frags == ['HCD']:
# hcd olny method
usefilts = self.cfgFilters['filt_hcd']
self.remove = self.cfgFilters['rem_hcd']
else:
# CID/PQD only method
usefilts = self.cfgFilters['filt_other']
self.remove = self.cfgFilters['rem_other']
else:
# mixed method
usefilts = self.cfgFilters['filt_mixed_hcd_other']
self.remove = self.cfgFilters['rem_mixed_hcd_other']
if len(self.isos) == 0:
repionIdx = -1
for idx in range(len(usefilts)):
if usefilts[idx] == 'repion':
repionIdx = idx
break
if repionIdx != -1:
usefilts.pop(repionIdx)
self.usefilts = usefilts
self.hdf5.close()
def close(self):
self.hdf5.close()
def getActivationTypes(self):
data = self.hdf5.getDataEqual('/rawdata/parameters', 'parameter',
'Activation Type')
if len(data) == 0:
data = self.hdf5.getDataEqual('/rawdata/parameters', 'parameter',
'activation')
types = {}
for act in data.flat:
activation = act['value'].upper()
types[activation] = types.get(activation, 0) + 1
return types.keys()
def export(self, hcdonly=0):
"""
@brief creates an mgf file for the MS/MS spectra in the hdf5 file
@param hcdonly <integer>: flag to switch output to only HCD spectra bypassing the normal export filters
"""
if hcdonly:
remove = ['CID']
filters = ['none']
else:
remove = self.remove
filters = self.usefilts
hdf = self.hdf5
mgfFile = hdf.filePath.parent.joinpath(hdf.filePath.stem + '.mgf')
# extra = path(hdf.filepath.splitext()[0] + '.txt')
# self.fextra = extra.open('w')
# self.fextra.write('spec_id\tmz\tinten\trel_inten\tion\texp_mz\n')
mgfOut = open(str(mgfFile), 'w')
mgfOut.write('#Removed spectra = %s, filtering = %s\n' %
(remove, filters))
spec = 0
# read parameters from hdf5 file
try:
hdf.appendOpen()
headers = hdf.readTable('/rawdata/msmsheader')
runTimeEntry = hdf.getDataEqual('/rawdata/parameters', 'parameter',
'MS Run Time (min)')
if len(runTimeEntry) == 0:
raise ExHa.MGFprocessingError(
'MGF Error: Could not find "MS Run Time (min)" parameter in HDF5 file.'
)
runtime = runTimeEntry[0]['value']
units = self.readUnitsOK()
# add new table for the deconvoluted spectrum data
hdf.removeTable('/rawdata/deconvions')
hdf.createTable('rawdata', 'deconvions', 'DeconvIons')
ident = []
for frag in units[1]:
# find all the frag methods to be used in identification
if 'I' in frag['use']:
ident.append(frag['order'])
logger.log.info('Reading %d spectra from %s' %
(len(headers), hdf.filePath.name))
if 'deconv' in filters:
deconv = 1
else:
deconv = 0
pBar = progBar.ProgressBar(widgets=progBar.name_widgets,
maxval=len(headers),
name='Create .mgf').start()
for idx, h in enumerate(headers):
if hcdonly:
if h['fragmeth'] != 'HCD':
continue
elif not h['order'] in ident:
continue
pBar.update(idx)
# get spectrum data
spec = h['spec_id']
spectrum = hdf.getDataEqual('/rawdata/ions', 'spec_id', spec)
if deconv:
# need extra column for charge information
spectrum = self.addChargeColumn(spectrum)
data = hdf.getDataGeneral(
'/rawdata/specparams',
'(spec_id == %i) & (parameter == "%s")' %
(spec, 'setmass1'))
setmass = data[0]['value']
data = hdf.getDataGeneral(
'/rawdata/specparams',
'(spec_id == %i) & (parameter == "%s")' % (spec, 'frag1'))
frag = data[0]['value']
try:
self.maxint = max(spectrum['inten'])
except:
self.maxint = 0
# construct title values list
rt = '%.3f' % h['rt']
use = units[1][h['order'] - 1]['use']
pretitle = ''
if use == 'IQ':
# spec is both ID and Quan so us normal msms ID
titles = ['msmsid:F%06d' % h['spec_id']]
elif use == 'I':
if h['quan_spec'] == 0:
# no quant data so use spec_id
titles = ['msmsid:F%06d' % h['spec_id']]
else:
# spec is only for ident find the quan spec
titles = ['msmsid:F%06d' % h['quan_spec']]
pretitle = '#CID=F%06d\n' % h['id_spec']
elif use == 'Q':
titles = ['msmsid:F%06d' % h['quan_spec']]
pretitle = '#CID=F%06d\n' % h['id_spec']
titles.append('rt:' + rt)
titles.append('survey:S%06d' % h['survey_spec'])
titles.append('parent:' + setmass)
titles.append('AnalTime:' + runtime)
titles.append('Activation:' + frag.upper())
titleline = 'TITLE=%s\n' % ','.join(titles)
if h['precmz'] > 0:
pepmass = h['precmz']
elif h['precmz_surv'] > 0:
pepmass = h['precmz_surv']
else:
pepmass = h['monomz']
if pepmass == 0:
continue
for filt in filters:
if len(spectrum) > 5 and self.filters[filt]:
spectrum = self.filters[filt](h, spectrum)
# filter for mascot interference
ionList = []
if len(spectrum) > 2:
mgfOut.write(pretitle)
mgfOut.write('BEGIN IONS\n')
mgfOut.write(titleline)
mgfOut.write('PEPMASS=%f\n' % pepmass)
mgfOut.write('CHARGE=%d+\n' % h['charge'])
if deconv:
for pt in spectrum:
if pt['inten'] == 0:
continue
mgfOut.write('%f %f %s\n' %
(pt['mz'], pt['inten'], pt['charge']))
ionList.append(
dict(spec_id=pt['spec_id'],
mz=pt['mz'],
inten=pt['inten'],
charge=pt['charge']))
else:
for pt in spectrum:
if pt['inten'] == 0:
continue
mgfOut.write('%f %f\n' % (pt['mz'], pt['inten']))
ionList.append(
dict(spec_id=pt['spec_id'],
mz=pt['mz'],
inten=pt['inten']))
mgfOut.write('END IONS\n\n')
if len(ionList) > 0:
hdf.appendRows('/rawdata/deconvions', ionList)
pBar.finish()
except ExHa.MGFprocessingError, czEx:
if spec:
ExHa.addContext(czEx,
'Raised whist processing spectrum %i' % spec)
raise
except Exception as genEx:
ExHa.reformatException(genEx)
if spec:
ExHa.addContext(genEx,
'Raised whist processing spectrum %i' % spec)
raise
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)
from pathlib import Path
# cellzome CommonUtils
sys.path.insert(0, '..')
from CommonUtils.tools import *
from CommonUtils.ConfigManager import pyMSsafeConfigManager
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
