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()