if not options.dtaDir or not options.model or not options.config:
print 'ERROR: missing model, config, or dtaDir'
exit(-1)
Constants.aminoacids['C'] = (Constants.aminoacids['C'][0], Constants.aminoacids['C'][1], Constants.aminoacids['C'][2] + Constants.mods['Carbamidomethyl'], Constants.aminoacids['C'][3])
Constants.aminoacids['O'] = (Constants.aminoacids['M'][0], Constants.aminoacids['M'][1] + 'O', Constants.aminoacids['M'][2] + Constants.mods['#'], Constants.aminoacids['M'][3])
if options.Cmod == Constants.mods['*']:
Constants.aminoacids['X'] = (Constants.aminoacids['K'][0], Constants.aminoacids['K'][1], Constants.aminoacids['K'][2] + Constants.mods['*'], Constants.aminoacids['K'][3])
PNet = PN.ProbNetwork(options.config, options.model)
if options.verbose:
t1 = time.time()
print 'Getting heavy-light pairs'
dtaList = glob.glob(options.dtaDir + '/*.dta')
(paired, unpaired) = Analytics.getPairedAndUnpairedSpectra(options.dtaDir, dtaList, delta=(options.Nmod + options.Cmod), ppm=options.ppm, cutOff=options.pairCutoff)
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)
