def main(args):
# debugging info
logfile = args.outDirName + "/" + args.outBaseName + "/logs/%d" % os.getpid() + "." + args.outBaseName + ".mergepairs.log"
logging.basicConfig(format='%(asctime)s %(message)s',filename=logfile,level=logging.DEBUG)
logging.info("\ninDir1=%s\ninDir2=%s\noutBaseName=%s\nconfigFileName=%s"
% (args.inDir1,args.inDir2,args.outBaseName,args.configFileName))
# create output directory
discordant.prepOutDir(args.outBaseName,args.outDirName,args.overwrite)
# make sure input sources exist
peakparser.checkOutDir(args.inDir1,args.outDirName)
peakparser.checkOutDir(args.inDir2,args.outDirName)
# make sure config files exist
configPath1 = args.outDirName + "/" + args.inDir1 + "/" + args.configFileName
configPath2 = args.outDirName + "/" + args.inDir2 + "/" + args.configFileName
discordant.checkfile(configPath1)
discordant.checkfile(configPath2)
# read parameters for both inputs
configDict1 = peakparser.readConfig(configPath1,args.inDir1,args.outDirName)
configDict2 = peakparser.readConfig(configPath2,args.inDir2,args.outDirName)
maxDist = int(configDict1['insertSize']) + 2*int(configDict1['readLength'])
eltLenDict = discordant.makeEltLenDict(configDict1['eltLenFileName'])
# merge readfiles
outReadFileName = args.outDirName + "/" + args.outBaseName + "/" + args.outBaseName + ".readpairs.txt"
readFileName1 = args.outDirName + "/" + args.inDir1 + "/" + args.inDir1 + ".readpairs.txt"
readFileName2 = args.outDirName + "/" + args.inDir2 + "/" + args.inDir2 + ".readpairs.txt"
logging.info("merging readfiles (%s, %s)" % (readFileName1,readFileName2))
# print "merging readfiles (%s, %s)" % (readFileName1,readFileName2)
mergeChrPosFiles(readFileName1,readFileName2,outReadFileName,maxDist,eltLenDict)
# merge bedfiles
outBedFileName = args.outDirName + "/" + args.outBaseName + "/" + args.outBaseName + ".reads.bed"
bedFileName1 = args.outDirName + "/" + args.inDir1 + "/" + args.inDir1 + ".reads.bed"
bedFileName2 = args.outDirName + "/" + args.inDir2 + "/" + args.inDir2 + ".reads.bed"
logging.info("merging bedfiles (%s,%s)" % (bedFileName1,bedFileName2))
# print "merging bedfiles (%s,%s)" % (bedFileName1,bedFileName2)
mergeChrPosFiles(bedFileName1,bedFileName2,outBedFileName,maxDist,eltLenDict)
# write new config file
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
configDict = configDict1
configDict['bamFileName1'] = configDict1['bamFileName']
configDict['bamFileName2'] = configDict2['bamFileName']
configDict['merged'] = 'True'
configDict['outBaseName'] = args.outBaseName
configDict['outDirName'] = args.outDirName
configDict['readFileName'] = outReadFileName
del configDict['bamFileName']
f = open(configPath, 'w')
for k,v in configDict.iteritems():
f.write(k + "=" + v + "\n")
f.close()
def main(args):
# create output directory
pickreads.prepOutDir(args.outBaseName,args.outDirName,args.overwrite)
pickreads.checkfile(args.sampleListFile)
sampleList = open(args.sampleListFile, 'r')
readFileNames = []
bamFileNames = []
insertSizes = []
readLengths = []
lastConfig = None
for sampleLine in sampleList:
if not re.search("^#", sampleLine):
(sampleBam,sampleSubDir,refGenome) = sampleLine.strip().split()
peakparser.checkOutDir(sampleSubDir,args.outDirName)
configPath = args.outDirName + "/" + sampleSubDir + "/" + args.configFileName
pickreads.checkfile(configPath)
configDict = peakparser.readConfig(configPath,sampleSubDir,args.outDirName)
lastConfig = configDict
insertSizes.append(int(configDict['insertSize']))
readLengths.append(int(configDict['readLength']))
readFileName = args.outDirName + "/" + sampleSubDir + "/" + sampleSubDir + ".readpairs.txt"
readFileNames.append(readFileName)
bamFileNames.append(configDict['bamFileName'])
maxDist = max(insertSizes) + 2*max(readLengths)
# merge readfiles
outReadFileName = args.outDirName + "/" + args.outBaseName + "/" + args.outBaseName + ".readpairs.txt"
mergeChrPosFiles(readFileNames,outReadFileName,maxDist)
# write new config file
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
configDict = lastConfig
bfnum = 0
for bamFileName in bamFileNames:
bfvname = "bamFileName" + str(bfnum)
configDict[bfvname] = bamFileName
bfnum += 1
configDict['merged'] = 'True'
configDict['outBaseName'] = args.outBaseName
configDict['outDirName'] = args.outDirName
configDict['readFileName'] = outReadFileName
del configDict['bamFileName']
f = open(configPath, 'w')
for k,v in configDict.iteritems():
f.write(k + "=" + v + "\n")
f.close()
def main(args):
peakparser.checkOutDir(args.outBaseName,args.outDirName)
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
discordant.checkfile(configPath)
configDict = peakparser.readConfig(configPath,args.outBaseName,args.outDirName)
refGenome = configDict['refGenome']
checkAnnotDir(refGenome, args.annotDir)
debugFile = args.outDirName + "/" + args.outBaseName + "/" + args.outBaseName + ".debug.txt"
discordant.checkfile(debugFile)
# can filter on retroelement subfamilies
discordant.checkfile(args.eltFile)
eltDict = {}
f = open(args.eltFile,'r')
for elt in f:
eltDict[elt.strip()]=1
germlineIns = []
cancerIns = []
normalIns = []
otherIns = []
f = open(debugFile, 'r')
for line in f: # loop over lines
if re.search('valid=1', line) and (re.search('olClN=0', line) or args.allowOverlap):
insdata = {}
for c in line.rstrip().rsplit(' '): # loop over columns
(key,value) = c.rsplit('=')
insdata[key] = value
if int(insdata['np']) >= int(args.minPeakSize) and eltDict.has_key(insdata['pME']):
insSum = insertionSummary()
insSum.setPos(insdata['pos'])
insSum.setEltPos(insdata['eltExt'])
insSum.setBestStrand(insdata['eInv'],insdata['eS'])
insSum.setSources(insdata['sources'])
insSum.setClassIndex(insdata['index'])
insSum.eltFam = insdata['pME']
insSum.numreads = insdata['np']
if len(insSum.sources) > 1:
germlineIns.append(insSum)
else:
if re.search('CANCER', insSum.sources[0]):
cancerIns.append(insSum)
elif re.search('NORMAL', insSum.sources[0]):
normalIns.append(insSum)
else:
otherIns.append(insSum)
f.close()
annotatePos(germlineIns,refGenome,args.annotDir,args.outDirName + "/" + args.outBaseName + "/germline.tab.txt",args.printout)
annotatePos(cancerIns,refGenome,args.annotDir,args.outDirName + "/" + args.outBaseName + "/canceronly.tab.txt",args.printout)
annotatePos(normalIns,refGenome,args.annotDir,args.outDirName + "/" + args.outBaseName + "/normalonly.tab.txt",args.printout)
annotatePos(otherIns,refGenome,args.annotDir,args.outDirName + "/" + args.outBaseName + "/other.tab.txt",args.printout)
def main(args):
peakparser.checkOutDir(args.outBaseName,args.outDirName)
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
checkfile(configPath)
configDict = peakparser.readConfig(configPath,args.outBaseName,args.outDirName)
refGenome = configDict['refGenome']
checkAnnotDir(refGenome,args.annotDir)
debugFile = args.outDirName + "/" + args.outBaseName + "/" + args.outBaseName + ".debug.txt"
checkfile(debugFile)
germlineIns = []
cancerIns = []
normalIns = []
uncatIns = []
f = open(debugFile, 'r')
for line in f: # loop over lines
if re.search('valid=1', line):
insdata = {}
for c in line.rstrip().rsplit(' '): # loop over columns
(key,value) = c.rsplit('=')
insdata[key] = value
if int(insdata['np']) >= 8 and int(insdata['nEx']) > 1:
insSum = insertionSummary()
insSum.setPos(insdata['pos'])
insSum.setEltPos(insdata['eltExt'])
insSum.setBestStrand(insdata['eInv'],insdata['eS'])
insSum.setSources(insdata['sources'])
insSum.index = insdata['index']
insSum.priGene = insdata['pGene']
insSum.exonStr = insdata['exT']
insSum.eltFam = insdata['pME']
insSum.numreads = insdata['np']
insSum.pseudo = insdata['pgO']
if len(insSum.sources) > 1:
germlineIns.append(insSum)
else:
if re.search('CANCER', insSum.sources[0]):
cancerIns.append(insSum)
elif re.search('NORMAL', insSum.sources[0]):
normalIns.append(insSum)
else:
uncatIns.append(insSum)
f.close()
annotatePos(germlineIns,refGenome,args.outDirName + "/" + args.outBaseName + "/germline.tab.txt",args.annotDir,args.printout)
annotatePos(cancerIns,refGenome,args.outDirName + "/" + args.outBaseName + "/canceronly.tab.txt",args.annotDir,args.printout)
annotatePos(normalIns,refGenome,args.outDirName + "/" + args.outBaseName + "/normalonly.tab.txt",args.annotDir,args.printout)
annotatePos(uncatIns,refGenome,args.outDirName + "/" + args.outBaseName + "/uncategorized.tab.txt",args.annotDir,args.printout)
def main(args):
# debugging info
logfile = args.outDirName + "/" + args.outBaseName + "/logs/%d" % os.getpid(
) + "." + args.outBaseName + ".mergepairs.log"
logging.basicConfig(format='%(asctime)s %(message)s',
filename=logfile,
level=logging.DEBUG)
logging.info(
"\ninDir1=%s\ninDir2=%s\noutBaseName=%s\nconfigFileName=%s" %
(args.inDir1, args.inDir2, args.outBaseName, args.configFileName))
# create output directory
pickreads.prepOutDir(args.outBaseName, args.outDirName, args.overwrite)
# make sure input sources exist
peakparser.checkOutDir(args.inDir1, args.outDirName)
peakparser.checkOutDir(args.inDir2, args.outDirName)
# make sure config files exist
configPath1 = args.outDirName + "/" + args.inDir1 + "/" + args.configFileName
configPath2 = args.outDirName + "/" + args.inDir2 + "/" + args.configFileName
pickreads.checkfile(configPath1)
pickreads.checkfile(configPath2)
# read parameters for both inputs
configDict1 = peakparser.readConfig(configPath1, args.inDir1,
args.outDirName)
configDict2 = peakparser.readConfig(configPath2, args.inDir2,
args.outDirName)
maxDist = int(
configDict1['insertSize']) + 2 * int(configDict1['readLength'])
# merge readfiles
outReadFileName = args.outDirName + "/" + args.outBaseName + "/" + args.outBaseName + ".readpairs.txt"
readFileName1 = args.outDirName + "/" + args.inDir1 + "/" + args.inDir1 + ".readpairs.txt"
readFileName2 = args.outDirName + "/" + args.inDir2 + "/" + args.inDir2 + ".readpairs.txt"
logging.info("merging readfiles (%s, %s)" % (readFileName1, readFileName2))
# print "merging readfiles (%s, %s)" % (readFileName1,readFileName2)
mergeChrPosFiles(readFileName1, readFileName2, outReadFileName, maxDist)
# merge bedfiles
outBedFileName = args.outDirName + "/" + args.outBaseName + "/" + args.outBaseName + ".reads.bed"
bedFileName1 = args.outDirName + "/" + args.inDir1 + "/" + args.inDir1 + ".reads.bed"
bedFileName2 = args.outDirName + "/" + args.inDir2 + "/" + args.inDir2 + ".reads.bed"
logging.info("merging bedfiles (%s,%s)" % (bedFileName1, bedFileName2))
# print "merging bedfiles (%s,%s)" % (bedFileName1,bedFileName2)
mergeChrPosFiles(bedFileName1, bedFileName2, outBedFileName, maxDist)
# write new config file
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
configDict = configDict1
configDict['bamFileName1'] = configDict1['bamFileName']
configDict['bamFileName2'] = configDict2['bamFileName']
configDict['merged'] = 'True'
configDict['outBaseName'] = args.outBaseName
configDict['outDirName'] = args.outDirName
configDict['readFileName'] = outReadFileName
del configDict['bamFileName']
f = open(configPath, 'w')
for k, v in configDict.iteritems():
f.write(k + "=" + v + "\n")
f.close()
def main(args):
peakparser.checkOutDir(args.outBaseName, args.outDirName)
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
checkfile(configPath)
configDict = peakparser.readConfig(configPath, args.outBaseName,
args.outDirName)
# load hash of TranscriptSeq objects (genename --> multiple transcripts)
# will need to pass to partialMapTx() later
sys.stderr.write("loading " + args.mrnaFastaFile + "...\n")
checkfile(args.mrnaFastaFile)
txs = fastahash(args.mrnaFastaFile)
cancerBamFile = ''
normalBamFile = ''
refGenomeFile = args.refGenomeFile
cancerCallsFile = args.outDirName + "/" + args.outBaseName + "/canceronly.tab.txt"
normalCallsFile = args.outDirName + "/" + args.outBaseName + "/normalonly.tab.txt"
germCallsFile = args.outDirName + "/" + args.outBaseName + "/germline.tab.txt"
otherCallsFile = args.outDirName + "/" + args.outBaseName + "/uncategorized.tab.txt"
# fix if unmerged
if not configDict.has_key('bamFileName1'):
configDict['bamFileName1'] = configDict['bamFileName']
configDict['bamFileName2'] = configDict['bamFileName']
bamType1 = getTypeFromTCGA(configDict['bamFileName1'])
bamType2 = getTypeFromTCGA(configDict['bamFileName2'])
print("bamfile1=%s bamFile2=%s bamType1=%s bamType2=%s" %
(configDict['bamFileName1'], configDict['bamFileName2'], bamType1,
bamType2))
if bamType1 != bamType2 and bamType1 != None and bamType2 != None:
if bamType1 == 'CANCER':
if bamType2 != 'NORMAL':
raise NameError('bam1 is cancer but bam2 is not normal')
cancerBamFile = configDict['bamFileName1']
normalBamFile = configDict['bamFileName2']
if bamType2 == 'CANCER':
if bamType1 != 'NORMAL':
raise NameError('bam2 is cancer but bam1 is not normal')
cancerBamFile = configDict['bamFileName2']
normalBamFile = configDict['bamFileName1']
else:
print 'cannot determine bamfile cancer/normal from filenames in config.txt, defaulting to normal.'
normalBamFile = configDict['bamFileName1']
cancerBamFile = configDict['bamFileName2']
checkfile(cancerBamFile)
checkfile(normalBamFile)
checkfile(normalCallsFile)
checkfile(cancerCallsFile)
checkfile(germCallsFile)
checkfile(otherCallsFile)
checkfile(refGenomeFile)
cancerBam = pysam.Samfile(cancerBamFile, 'rb') # rb = read, binary
normalBam = pysam.Samfile(normalBamFile, 'rb') # rb = read, binary
cancerCalls = open(cancerCallsFile, 'r')
normalCalls = open(normalCallsFile, 'r')
germCalls = open(germCallsFile, 'r')
otherCalls = open(otherCallsFile, 'r')
refGenome = pysam.Fastafile(refGenomeFile)
cancerBreaksOut = open(
args.outDirName + "/" + args.outBaseName + "/cancerbreaks.tab.txt",
'w')
normalBreaksOut = open(
args.outDirName + "/" + args.outBaseName + "/normalbreaks.tab.txt",
'w')
germBreaksOut = open(
args.outDirName + "/" + args.outBaseName + "/germlinebreaks.tab.txt",
'w')
otherBreaksOut = open(
args.outDirName + "/" + args.outBaseName +
"/uncategorizedbreaks.tab.txt", 'w')
callSetListNames = ('cancer', 'normal', 'germ', 'other')
callSetListInFiles = (cancerCalls, normalCalls, germCalls, otherCalls)
callSetListOutFiles = (cancerBreaksOut, normalBreaksOut, germBreaksOut,
otherBreaksOut)
for i in range(len(callSetListNames)):
for line in callSetListInFiles[i]:
col = line.strip().split("\t")
chr = col[0]
start = int(col[1])
end = int(col[2])
gene = col[7]
cancerCluster = fetchRegion(cancerBam, refGenome,
int(args.maxReadLen), chr, start, end,
gene, args.zeroChar,
int(args.minClipQual), args.usechr)
cancerCluster.type = 'CANCER'
normalCluster = fetchRegion(normalBam, refGenome,
int(args.maxReadLen), chr, start, end,
gene, args.zeroChar,
int(args.minClipQual), args.usechr)
normalCluster.type = 'NORMAL'
mergeCluster = mergeClusters(cancerCluster, normalCluster, txs)
clusterout = mergeCluster.outstring()
infodumpout = mergeCluster.infodump()
callSetListOutFiles[i].write(
line.strip("\n") + "\t" + clusterout + "\n" + infodumpout +
"\n")
callSetListInFiles[i].close()
callSetListOutFiles[i].close()
def main(args):
peakparser.checkOutDir(args.outBaseName,args.outDirName)
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
checkfile(configPath)
configDict = peakparser.readConfig(configPath,args.outBaseName,args.outDirName)
cancerBamFile = ''
normalBamFile = ''
refGenomeFile = args.refGenomeFile
cancerCallsFile = args.outDirName + "/" + args.outBaseName + "/canceronly.tab.txt"
normalCallsFile = args.outDirName + "/" + args.outBaseName + "/normalonly.tab.txt"
germCallsFile = args.outDirName + "/" + args.outBaseName + "/germline.tab.txt"
otherCallsFile = args.outDirName + "/" + args.outBaseName + "/other.tab.txt"
# fix if unmerged
if not configDict.has_key('bamFileName1'):
configDict['bamFileName1'] = configDict['bamFileName']
configDict['bamFileName2'] = configDict['bamFileName']
bamType1 = getTypeFromTCGA(configDict['bamFileName1'])
bamType2 = getTypeFromTCGA(configDict['bamFileName2'])
print ("bamfile1=%s bamFile2=%s bamType1=%s bamType2=%s"
% (configDict['bamFileName1'], configDict['bamFileName2'], bamType1, bamType2))
if bamType1 != bamType2 and bamType1 != None and bamType2 != None:
if bamType1 == 'CANCER':
if bamType2 != 'NORMAL':
raise NameError('bam1 is cancer but bam2 is not normal')
cancerBamFile = configDict['bamFileName1']
normalBamFile = configDict['bamFileName2']
if bamType2 == 'CANCER':
if bamType1 != 'NORMAL':
raise NameError('bam2 is cancer but bam1 is not normal')
cancerBamFile = configDict['bamFileName2']
normalBamFile = configDict['bamFileName1']
else:
print 'cannot determine bamfile cancer/normal from filenames in config.txt, defaulting to normal.'
normalBamFile = configDict['bamFileName1']
cancerBamFile = configDict['bamFileName2']
checkfile(cancerBamFile)
checkfile(normalBamFile)
checkfile(normalCallsFile)
checkfile(cancerCallsFile)
checkfile(germCallsFile)
checkfile(otherCallsFile)
checkfile(refGenomeFile)
cancerBam = pysam.Samfile(cancerBamFile, 'rb') # rb = read, binary
normalBam = pysam.Samfile(normalBamFile, 'rb') # rb = read, binary
cancerCalls = open(cancerCallsFile, 'r')
normalCalls = open(normalCallsFile, 'r')
germCalls = open(germCallsFile, 'r')
otherCalls = open(otherCallsFile, 'r')
refGenome = pysam.Fastafile(refGenomeFile)
cancerBreaksOut = open(args.outDirName + "/" + args.outBaseName + "/cancerbreaks.tab.txt", 'w')
normalBreaksOut = open(args.outDirName + "/" + args.outBaseName + "/normalbreaks.tab.txt", 'w')
germBreaksOut = open(args.outDirName + "/" + args.outBaseName + "/germlinebreaks.tab.txt", 'w')
otherBreaksOut = open(args.outDirName + "/" + args.outBaseName + "/otherbreaks.tab.txt", 'w')
callSetListNames = ('cancer', 'normal', 'germ','other')
callSetListInFiles = (cancerCalls, normalCalls, germCalls, otherCalls)
callSetListOutFiles = (cancerBreaksOut, normalBreaksOut, germBreaksOut, otherBreaksOut)
for i in range(len(callSetListNames)):
for line in callSetListInFiles[i]:
col = line.strip().split("\t")
chr = col[0]
start = int(col[1])
end = int(col[2])
cancerCluster = fetchRegion(cancerBam,refGenome,int(args.maxReadLen),chr,start,end,args.zeroChar,int(args.minClipQual),args.usechr)
cancerCluster.type='CANCER'
normalCluster = fetchRegion(normalBam,refGenome,int(args.maxReadLen),chr,start,end,args.zeroChar,int(args.minClipQual),args.usechr)
normalCluster.type='NORMAL'
mergeCluster = mergeClusters(cancerCluster,normalCluster,args.refFastaDir)
clusterout = mergeCluster.outstring()
infodumpout = mergeCluster.infodump()
callSetListOutFiles[i].write(line.strip("\n") + "\t" + clusterout + "\n" + infodumpout + "\n")
callSetListInFiles[i].close()
callSetListOutFiles[i].close()
def main(args):
peakparser.checkOutDir(args.outBaseName,args.outDirName)
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
checkfile(configPath)
configDict = peakparser.readConfig(configPath,args.outBaseName,args.outDirName)
cancerBamFile = ''
normalBamFile = ''
refGenomeFile = args.refGenomeFile
cancerCallsFile = args.outDirName + "/" + args.outBaseName + "/canceronly.tab.txt"
normalCallsFile = args.outDirName + "/" + args.outBaseName + "/normalonly.tab.txt"
germCallsFile = args.outDirName + "/" + args.outBaseName + "/germline.tab.txt"
otherCallsFile = args.outDirName + "/" + args.outBaseName + "/other.tab.txt"
bamFiles = []
sampleNames = []
for key in configDict.keys():
if key.startswith('bamFileName'):
bamFiles.append(configDict[key])
samplekey = "sampleName" + re.sub('bamFileName','',key)
sampleNames.append(configDict[samplekey])
print "finding breakpoints from bam files:"
for i in range(len(bamFiles)):
print bamFiles[i], sampleNames[i]
for bamFile in bamFiles:
checkfile(bamFile)
checkfile(normalCallsFile)
checkfile(cancerCallsFile)
checkfile(germCallsFile)
checkfile(otherCallsFile)
checkfile(refGenomeFile)
bamPysams = []
for bamFile in bamFiles:
bamPysam = pysam.Samfile(bamFile, 'rb')
bamPysams.append(bamPysam)
cancerCalls = open(cancerCallsFile, 'r')
normalCalls = open(normalCallsFile, 'r')
germCalls = open(germCallsFile, 'r')
otherCalls = open(otherCallsFile, 'r')
refGenome = pysam.Fastafile(refGenomeFile)
cancerBreaksOut = open(args.outDirName + "/" + args.outBaseName + "/cancerbreaks.tab.txt", 'w')
normalBreaksOut = open(args.outDirName + "/" + args.outBaseName + "/normalbreaks.tab.txt", 'w')
germBreaksOut = open(args.outDirName + "/" + args.outBaseName + "/germlinebreaks.tab.txt", 'w')
otherBreaksOut = open(args.outDirName + "/" + args.outBaseName + "/otherbreaks.tab.txt", 'w')
callSetListNames = ('cancer', 'normal', 'germ','other')
callSetListInFiles = (cancerCalls, normalCalls, germCalls, otherCalls)
callSetListOutFiles = (cancerBreaksOut, normalBreaksOut, germBreaksOut, otherBreaksOut)
for i in range(len(callSetListNames)):
for line in callSetListInFiles[i]:
col = line.strip().split("\t")
chr = col[0]
start = int(col[1])
end = int(col[2])
mergedCluster = fetchRegion(bamPysams[0],refGenome,int(args.maxReadLen),chr,start,end,args.zeroChar,int(args.minClipQual),args.usechr)
mergedCluster.type=sampleNames[0]
for p in range(1,len(bamPysams)):
nextCluster = fetchRegion(bamPysams[p],refGenome,int(args.maxReadLen),chr,start,end,args.zeroChar,int(args.minClipQual),args.usechr)
nextCluster.type=sampleNames[p]
mergedCluster = mergeClusters(mergedCluster,nextCluster,args.refFastaDir)
clusterout = mergedCluster.outstring()
infodumpout = mergedCluster.infodump()
callSetListOutFiles[i].write(line.strip("\n") + "\t" + clusterout + "\n" + infodumpout + "\n")
callSetListInFiles[i].close()
callSetListOutFiles[i].close()
def main(args):
peakparser.checkOutDir(args.outBaseName, args.outDirName)
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
checkfile(configPath)
configDict = peakparser.readConfig(configPath, args.outBaseName,
args.outDirName)
refGenome = configDict['refGenome']
checkAnnotDir(refGenome, args.annotDir)
debugFile = args.outDirName + "/" + args.outBaseName + "/" + args.outBaseName + ".debug.txt"
checkfile(debugFile)
germlineIns = []
cancerIns = []
normalIns = []
uncatIns = []
f = open(debugFile, 'r')
for line in f: # loop over lines
if re.search('valid=1', line):
insdata = {}
for c in line.rstrip().rsplit(' '): # loop over columns
(key, value) = c.rsplit('=')
insdata[key] = value
if int(insdata['np']) >= int(args.minPeakSize) and int(
insdata['nEx']) > 1:
insSum = insertionSummary()
insSum.setPos(insdata['pos'])
insSum.setEltPos(insdata['eltExt'])
insSum.setBestStrand(insdata['eInv'], insdata['eS'])
insSum.setSources(insdata['sources'])
insSum.index = insdata['index']
insSum.priGene = insdata['pGene']
insSum.exonStr = insdata['exT']
insSum.eltFam = insdata['pME']
insSum.numreads = insdata['np']
insSum.pseudo = insdata['pgO']
if len(insSum.sources) > 1:
germlineIns.append(insSum)
else:
if re.search('CANCER', insSum.sources[0]):
cancerIns.append(insSum)
elif re.search('NORMAL', insSum.sources[0]):
normalIns.append(insSum)
else:
uncatIns.append(insSum)
f.close()
annotatePos(germlineIns, refGenome,
args.outDirName + "/" + args.outBaseName + "/germline.tab.txt",
args.annotDir, args.printout)
annotatePos(
cancerIns, refGenome,
args.outDirName + "/" + args.outBaseName + "/canceronly.tab.txt",
args.annotDir, args.printout)
annotatePos(
normalIns, refGenome,
args.outDirName + "/" + args.outBaseName + "/normalonly.tab.txt",
args.annotDir, args.printout)
annotatePos(
uncatIns, refGenome,
args.outDirName + "/" + args.outBaseName + "/uncategorized.tab.txt",
args.annotDir, args.printout)
def main(args):
# create output directory
discordant.prepOutDir(args.outBaseName,args.outDirName,args.overwrite)
sampleList = []
try:
sampleList = args.sampleList
except AttributeError:
discordant.checkfile(args.sampleListFile)
sampleList = open(args.sampleListFile, 'r')
readFileNames = []
bamFileNames = []
sampleNames = []
insertSizes = []
readLengths = []
eltLenDict = None
lastConfig = None
for sampleLine in sampleList:
if not re.search("^#", sampleLine):
(sampleBam,sampleSubDir,refGenome,groupName) = sampleLine.strip().split()
peakparser.checkOutDir(sampleSubDir,args.outDirName)
configPath = args.outDirName + "/" + sampleSubDir + "/" + args.configFileName
discordant.checkfile(configPath)
configDict = peakparser.readConfig(configPath,sampleSubDir,args.outDirName)
eltLenDict = discordant.makeEltLenDict(configDict['eltLenFileName'])
lastConfig = configDict
insertSizes.append(int(configDict['insertSize']))
readLengths.append(int(configDict['readLength']))
readFileName = args.outDirName + "/" + sampleSubDir + "/" + sampleSubDir + ".readpairs.txt"
readFileNames.append(readFileName)
bamFileNames.append(configDict['bamFileName'])
sampleNames.append(sampleSubDir)
maxDist = max(insertSizes) + 2*max(readLengths)
# merge readfiles
outReadFileName = args.outDirName + "/" + args.outBaseName + "/" + args.outBaseName + ".readpairs.txt"
mergeChrPosFiles(readFileNames,outReadFileName,maxDist,eltLenDict)
# write new config file
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
configDict = lastConfig
assert len(bamFileNames) == len(sampleNames)
bfnum = 0
for bamFileName in bamFileNames:
bfvname = "bamFileName" + str(bfnum)
configDict[bfvname] = bamFileName
bfnum += 1
snum = 0
for sampleName in sampleNames:
samname = "sampleName" + str(snum)
configDict[samname] = sampleName
snum += 1
configDict['merged'] = 'True'
configDict['outBaseName'] = args.outBaseName
configDict['outDirName'] = args.outDirName
configDict['readFileName'] = outReadFileName
del configDict['bamFileName']
f = open(configPath, 'w')
for k,v in configDict.iteritems():
f.write(k + "=" + v + "\n")
f.close()
