# for scanF in samePeptideClusters[pair[0]] + samePeptideClusters[pair[1]]: # scanFDict[scanF]['sequenced'] = True # if options.output: # for pair in [(lightScanF, heavyScanF) for lightScanF in samePeptideClusters[pair[0]] for heavyScanF in samePeptideClusters[pair[1]]]: # scanData['light scan'] = int(pair[0]) # scanData['heavy scan'] = int(pair[1]) # outFile.write('\t'.join([str(scanData[col]) for col in cols]) + '\n') # else: # print 'WARNING: Invalid sequence! Unsuccessful sequencing of %s and %s with pair configuration %s' % (str(samePeptideClusters[pair[0]]), str(samePeptideClusters[pair[1]]), pairConfigName) # print '\nTime Taken:', time.time() - s1, '\n' if len(paramsDict['Pair Configurations'].keys()) == 0: unpaired = glob.glob(options.dtadir + '/*.dta') addEnds = DNS.getSpectrumGraphEndpointInitFunction(np.array(Constants.NTermMods.values()), np.array(Constants.CTermMods.values()), paramsDict['Enzyme']['specificity']) termModHash = Constants.createTermModHashAAs(N=Constants.NTermMods, C=Constants.CTermMods) # hyperParameters = PNet.getHyperParameters(None) # ambigPenaltyFun = DNS.getAmbigEdgePenaltyFunction(hyperParameters['minedge'], hyperParameters['ambigopen'], hyperParameters['ambigextend']) # ppmPenaltyFun = DNS.getPPMPenaltyFun(hyperParameters['ppmstd'], hashedAAs, hyperParameters['minedge'], hyperParameters['ppmpen'], 0, epStep) for cluster in samePeptideClusters: if scanFDict[cluster[0]]['sequenced'] or True: continue scanData = {} specsInfo = [DataFile.getMassIntPairs(scanFDict[scanF]['dta']) for scanF in cluster] precMass = np.average(np.array([scanFDict[scanF]['precMass'] for scanF in cluster])) scanData['light scan'] = None scanData['heavy scan'] = 'N/A'
aas = Constants.addPepsToAADict(options.minedge) hashedAAs = Constants.hashAAsEpsilonRange(aas, epStep, maxEp) ambigOpenPenalty = 0 ambigPenaltyFun = DNS.getAmbigEdgePenaltyFunction(options.minedge, ambigOpenPenalty, options.ambigpenalty) ppmPenaltyFun = DNS.getPPMPenaltyFun( options.ppmstd, hashedAAs, options.minedge, options.ppmpenalty, options.ppmsyserror, epStep ) addEnds = DNS.getSpectrumGraphEndpointInitFunction( np.array(Constants.NTermMods.values()), np.array(Constants.CTermMods.values()), paramsDict["Enzyme"]["specificity"], ) termModHash = Constants.createTermModHashAAs( N=copy.deepcopy(Constants.NTermMods), C=copy.deepcopy(Constants.CTermMods) ) print "Getting Pairs..." pairs = getCIDETDPairs(scanFDict) for pair in pairs: scanData = {} precMass = scanFDict[pair[0]]["precMass"] epMean = options.ppmsyserror * precMass * 10 ** -6 epSTD = options.ppmstd * precMass * 10 ** -6 # (lightPath, heavyPath) = (scanFDict[pair[0]]['dta'], scanFDict[pair[1]]['dta']) # scanData['shared peaks ratio'] = getSharedPeaksRatio(lightPath, heavyPath, epSTD) scanData["shared peaks ratio"] = "N/A"