def __init__(self, filedic, hdf5, cfg, logs, searchID, quantMethod):
'''
@brief initialise the Datfile object
@param filedic <dictionary>: containig the full path to the dat file and other file data
@param hdf5 <hdf5 object>: containing all the writing methods for hdf5 output
@param cfg <cfg object>: containing all the running parameters
@param dbobj <db object>: linking to the meet database
'''
self.filedic = filedic
self.searchid = searchID
self.quantMethod = quantMethod
datfilename = filedic['dat']
if datfilename == str(None):
raise ExHa.FileNotFoundException('no resulting datfile found with search')
self.datfilename = datfilename
self.cfg = cfg
self.logs = logs
self.hdfMascot = hdf5
self.dataDir = filedic['datpath'].parent
self.spectra = {}
self.peptidecounter = 0
self.failedsequences = 0
self.sequences = {}
self.seq2acc = {}
self.hookpeps = []
self.hookppm = []
self.analtimes = dict(first=40, last=0, early=[])
self.stats = dict(numpeps=0, numfailedpeps=0, numspectra_nopeps=0)
msg = 'merged sample'
else:
isMerged = False
msg = 'single sample'
importer = DATimporter(cfg, logger)
logger.log.info(msg)
searchDict = {}
for idx, hdf5file in enumerate(searches):
searchData = {}
searchData['hdf5name'] = hdf5file
searchData['archivepath'] = cfg.parameters['runtime']['datadir']
fullPath = searchData['archivepath']
fi = fullPath.joinpath(searchData['hdf5name'])
if not fi.exists():
raise ExHa.FileNotFoundException('Missing file: %s' % str(fi))
logger.log.info('Reading: %s' % str(fi))
importer.addHDFfile(fi, idx + 1, logger)
sw.rec('file loading')
fdrthreshold = cfg.parameters['general']['fdrthreshold']
peptidescoreatthreshold, score2fdr = importer.calculateFDR(
importer.setsManager.FDRdata, fdrthreshold)
importer.importData.score2fdr = score2fdr
importer.finaliseProteins(peptidescoreatthreshold)
proteinscoreatthreshold, score2fdr = importer.calculateFDR(
importer.setsManager.proteinFDRdata, fdrthreshold)
importer.importData.proteinscore2fdr = score2fdr
finalMessage = importer.updateHDF5()