scanData['shared peaks ratio'] = xVals[i][1]
print 'Now sequencing light scan(s) %s, heavy scan(s) %s with shared peaks ratio %f \n' % (str(samePeptideClusters[pair[0]]), str(samePeptideClusters[pair[1]]), xVals[i][1])
s1 = time.time()
sharedInfo, starts, ends, deltas, G = DNS.prepPairedSpectrumGraph(lightSpecs, heavySpecs, precMass, addEnds, ppmSTD=options.ppmstd, Nmod=pairConfig['NMod'], Cmod=pairConfig['CMod'], verbose=options.verbose)
scanData['M+H'] = precMass
specs = []
for massIntPairs in lightSpecs:
specs += [PN.Spectrum(PNet, precMass, Nmod=0.0, Cmod=0.0, epsilon=2*epSTD, spectrum=massIntPairs)]
for massIntPairs in heavySpecs:
specs += [PN.Spectrum(PNet, precMass + pairConfig['NMod'] + pairConfig['CMod'], Nmod=pairConfig['NMod'], Cmod=pairConfig['CMod'], epsilon=2*epSTD, spectrum=massIntPairs)]
for spec in specs:
spec.initializeNoiseModel()
scanData.update(DNS.getSpectrumGraphDataBlindMods(G, deltas, specs, starts, ends, precMass - Constants.mods['H+'] - Constants.mods['H2O'], ambigPenaltyFun, ppmPenaltyFun, hashedAAs, hashedMods, modAAsDict, termModHash=termModHash, modAlpha=options.modalpha, maxEdge=options.maxedge, minEdge=options.minedge, subGraphCut=options.subgraphcut, subAlpha=0.3, alpha=options.alpha, epMean=epMean, epSTD=epSTD, epStep=epStep, verbose=options.verbose))
scanData['sequencing time'] = time.time() - s1
scanData['pair configuration'] = pairConfigName
if validateHeavySequence(scanData['seq'], heavySeqMap, scanData['ambiguous edges']):
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:
