# print 'precMassClusters', precMassClusters
samePeptideClusters = Analytics.getSamePeptideClusters(precMassClusters, scanFDict, clusterSVMModel, clusterSVMRanges, ppmSTD=options.ppmstd, cutOff=float(paramsDict['Cluster Configuration']['cutoff']))
# samePeptideClusters = Analytics.getSamePeptideClusters(precMassClusters, scanFDict, clusterSVMModel, clusterSVMRanges, ppmSTD=options.ppmstd, cutOff=4)
# samePeptideClusters = An.getSamePeptideClusters(precMassClusters, scanFDict, clusterSVMModel, clusterSVMRanges, ppmSTD=options.ppmstd, cutOff=4)
# To test without any clustering
#samePeptideClusters = [[scanF] for scanF in scanFDict]
for pairConfigName in paramsDict['Pair Configurations']:
print 'Getting heavy-light pairs for %s' % (pairConfigName,)
t1 = time.time()
pairConfig = paramsDict['Pair Configurations'][pairConfigName]
pairs = Analytics.findDeltaPairsClusters(samePeptideClusters, scanFDict, pairConfig['NMod']+pairConfig['CMod'], ppm=options.ppmstd)
addEnds = DNS.getSpectrumGraphEndpointInitFunction(pairConfig['NStatic'], pairConfig['CStatic'], paramsDict['Enzyme']['specificity'])
termModHash = Constants.getTermModHashForPairConfig(pairConfig)
svmModel = svmutil.svm_load_model(parent + pairConfig['Model'])
svmRange = svmutil.load_ranges(parent + os.path.splitext(pairConfig['Model'])[0] + '.range')
xVals = []
# xVals = getPairsThread(pairs)
for pair in pairs:
lightSpecs = [DataFile.getMassIntPairs(scanFDict[lightScanF]['dta']) for lightScanF in samePeptideClusters[pair[0]]]
heavySpecs = [DataFile.getMassIntPairs(scanFDict[heavyScanF]['dta']) for heavyScanF in samePeptideClusters[pair[1]]]
lightPrecMass = np.average(np.array([scanFDict[lightScanF]['precMass'] for lightScanF in samePeptideClusters[pair[0]]]))
epSTD = options.ppmstd * 10 ** -6 * lightPrecMass
lightMergedSpec = SA.mergeSpectra(lightSpecs, epsilon=2*epSTD)
ETDPNet = PN.ProbNetwork(paramsDict["Models"]["etd"]["config"], paramsDict["Models"]["etd"]["model"])
HCDPNet = PN.ProbNetwork(paramsDict["Models"]["hcd"]["config"], paramsDict["Models"]["hcd"]["model"])
dtaList = glob.glob(options.dtadir + "/*.dta")
scanFDict = getScanFDict(dtaList)
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
