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
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()
