if options.verbose:
t2 = time.time()
print 'Finished getting paired spectra. Time taken: ', t2 - t1
print 'Starting Sequencing'
aas = Constants.addPepsToAADict(options.minEdge)
for pair in paired:
(lightSpec, heavySpec) = pair[1:]
if options.verbose:
print 'Now sequencing %s %s with shared peaks ratio %f' % (lightSpec, heavySpec, pair[0])
s1 = time.time()
heavyPath = heavySpec
lightPath = lightSpec
sharedInfo = DNS.getPairedSpectraInfoForSequencing(lightPath, heavyPath, options.verbose)
DNS.sequencePairedSpectra(sharedInfo['NInd'], sharedInfo['CInd'], sharedInfo['lightPairs'], sharedInfo['heavyPairs'], sharedInfo['lightPrecMass'] - Constants.mods['H+'] - Constants.mods['H2O'], PNet, alpha=options.alpha, unknownPenalty=options.ambigEdgePenalty, maxEdge=options.maxEdge, minEdge=options.minEdge, Nmod=options.Nmod, Cmod=options.Cmod, aas=aas, verbose=options.verbose)
if options.verbose:
print 'Time taken:', time.time() - s1
for spec in unpaired:
if options.verbose:
print 'Now sequencing unpaired spectrum %s' % spec
s1 = time.time()
precMass = DataFile.getPrecMassAndCharge(spec)[0]
pairs = DataFile.getMassIntPairs(spec)
DNS.sequenceSingleSpectrum(pairs, precMass - Constants.mods['H+'] - Constants.mods['H2O'], PNet, alpha=options.alpha, unknownPenalty=options.ambigEdgePenalty, maxEdge=options.maxEdge, minEdge=options.minEdge, aas=aas, verbose=options.verbose)
if options.verbose:
print 'Time taken:', time.time() - s1
