def adjustOpticalMap(contigMapFile, opticalMapFileOrig, opticalMapFileNew):
# Perform an initial alignment of of the contigMapFile against the opticalMapFile
outputPfx = '%s.%s.alignForAdjustment'%(contigMapFile,opticalMapFileOrig)
res = makeAlignments(opticalMapFileOrig, contigMapFile, outputPfx)
ml = parseSomaMatch.parseMatchFileXML(res['xmlFile'])
sys.stderr.write('adjustOpticalMap: Parsed %i matches from file %s\n'%(len(ml), res['xmlFile']))
# Filter the match list:
minHits = 10
maxMissRate = 0.10
def matchOK(mr):
hitsOK = mr.contigHits >= minHits
missRateOK = max(mr.contigMissRate, mr.opticalMissRate) <= maxMissRate
return hitsOK and missRateOK
goodMatches = [mr for mr in ml if matchOK(mr)]
sys.stderr.write('adjustOpticalMap: Filtered to %i matches based on quality'%(len(goodMatches)))
# Count the number of good alignments per contig. Only select the unique alignments
contigAlignmentCounts = Counter(mr.contigId for mr in goodMatches)
uniqueAlignments = [mr for mr in goodMatches if contigAlignmentCounts[mr.contigId]==1]
sys.stderr.write('adjustOpticalMap: Filtered to %i matches based on uniqueness'%(len(uniqueAlignments)))
# Create a matched chunk file
matchedChunkFile = '%s.matchedChunks'%outputPfx
adjustOpticalMaps.makeMatchedChunkFile(uniqueAlignments, matchedChunkFile)
adjustOpticalMaps.run(opticalMapFileOrig, matchedChunkFile, opticalMapFileNew)
def parseRandomAlignments(xmlFile):
numFrags = int(xmlFile.split('.')[1])
matchResults = parseSomaMatch.parseMatchFileXML(xmlFile)
ml = matchResults
matchDict = dict( (mr.contigId, mr) for mr in matchResults)
resDict = {}
resDict['matchDict'] = matchDict
resDict['chunkScores'] = [chunkScore for mr in ml for chunkScore in mr.getChunkScores()]
resDict['scores'] = [mr.score for mr in ml]
return resDict
def postProcess(xmlFile, opticalMapFile, contigMapFile, outputPfx):
# Parse results
print '\n'+'*'*50
print 'Parsing SOMA OUTPUT...'
print '*'*50 + '\n'
pickleFileAll = '%s.matchList.all.pickle'%outputPfx
pickleFileSig = '%s.matchList.sig.pickle'%outputPfx
pickleFileSigUnique = '%s.matchList.sig.unique.pickle'%outputPfx
# Parse Match Results. Write Pickle Files
ml = parseSomaMatch.parseMatchFileXML(xmlFile)
significanceTest.runSignificanceTest(ml, contigMapFile, opticalMapFile, numThreads=numThreads)
# Select significant results
pvalCutoff = 0.05
sigMatches = [mr for mr in ml if mr.pval <= pvalCutoff]
sigMatchDict = parseSomaMatch.collectMatchResultsByContig(sigMatches)
sigUniqueMatches = [matches[0] for contigId, matches in sigMatchDict.iteritems() if len(matches)==1]
sigUniqueMatchDict = parseSomaMatch.collectMatchResultsByContig(sigUniqueMatches)
sys.stdout.write('Found %i significant matches (%i bp)\n'%(len(sigMatches), sum(mr.cAlignedBases for mr in sigMatches)))
sys.stdout.write('Found %i unique significant matches (%i bp)\n'%(len(sigUniqueMatches), sum(mr.cAlignedBases for mr in sigUniqueMatches)))
# Pickle the matchResults
cPickle.dump(ml, open(pickleFileAll, 'w'))
cPickle.dump(sigMatches, open(pickleFileSig, 'w'))
cPickle.dump(sigUniqueMatches, open(pickleFileSigUnique, 'w'))
infoFileOut = '%s.info'%outputPfx
parseSomaMatch.writeInfoFile2(ml, infoFileOut)
# Summarize alignment status for contigs in the silicoFile
contigMapDict = SOMAMap.readMaps(contigMapFile)
opMapDict= SOMAMap.readMaps(opticalMapFile)
summarizeContigStatus.summarizeContigStatus(outputPfx, sigMatchDict, contigMapDict)
# Print all of the alignments to a textFile
fout = open('%s.SigUniqueAlignments.txt'%outputPfx, 'w')
parseSomaMatch.printAlignments(sigUniqueMatches, fout)
fout.close()
fout = open('%s.AllSigAlignments.txt'%outputPfx, 'w')
parseSomaMatch.printAlignments(sigMatches, fout)
fout.close()
# Create scaffolds
print '\n'+'*'*50
print 'Creating Scaffolds...'
print '*'*50 + '\n'
createScaffolds.createScaffolds(sigMatchDict, opMapDict, '%s.scaffold_sigMatches_withOverlaps.txt'%outputPfx, allowOverlaps=True)
createScaffolds.createScaffolds(sigMatchDict, opMapDict, '%s.scaffold_sigMatches_noOverlaps.txt'%outputPfx, allowOverlaps=False)
createScaffolds.createScaffolds(sigUniqueMatchDict, opMapDict, '%s.scaffold_sigUniqueMatches_withOverlaps.txt'%outputPfx, allowOverlaps=True)
createScaffolds.createScaffolds(sigUniqueMatchDict, opMapDict, '%s.scaffold_sigUniqueMatches_noOverlaps.txt'%outputPfx, allowOverlaps=False)
