aas = Constants.addPepsToAADict(300)
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)
print 'Getting Clusters'
parent = os.path.abspath(os.pardir)
clusterSVMModel = svmutil.svm_load_model(parent + paramsDict['Cluster Configuration']['model'])
clusterSVMRanges = svmutil.load_ranges(parent + os.path.splitext((paramsDict['Cluster Configuration']['model']))[0] + '.range')
precMassClusters = Analytics.findSamePrecMassClusters(dtaList, ppm=options.ppmstd)
# 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)
pairs = {}
times = {}
t1 = time.time()
print "Getting Clusters"
clusterSVMModel = svmutil.svm_load_model(paramsDict["Cluster Configuration"]["model"])
clusterSVMRanges = svmutil.load_ranges(
os.path.splitext((paramsDict["Cluster Configuration"]["model"]))[0] + ".range"
)
precMassClusters = An.findSamePrecMassClusters(dtaList, ppm=options.ppmstd)
# print 'precMassClusters', precMassClusters
samePeptideClusters = An.getSamePeptideClusters(
precMassClusters,
scanFDict,
clusterSVMModel,
clusterSVMRanges,
ppmSTD=options.ppmstd,
cutOff=float(paramsDict["Cluster Configuration"]["cutoff"]),
)
# samePeptideClusters = An.getSamePeptideClusters(precMassClusters, scanFDict, clusterSVMModel, clusterSVMRanges, ppmSTD=options.ppmstd, cutOff=4)
outFile.write("\n%i Clusters Found. Time taken: %f\n" % (len(samePeptideClusters), time.time() - t1))
trueClusters = An.getTrueClusters(
processedInfo[progName], dbDict["infoMap"], progDict, progName=progName, isComp=False, ppm=options.ppmstd
)
"""
clusteredScanFs = set()
nonUniqueClusteredScanFs = []
for cluster in trueClusters:
if len(cluster & clusteredScanFs) > 0:
print 'ERROR: Duplicate ScanFs in true clusters at cluster', cluster
clusteredScanFs = clusteredScanFs | cluster
