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)
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')