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):
# 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):
checkOutDir(args.outBaseName, args.outDirName)
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
pickreads.checkfile(configPath)
configDict = readConfig(configPath, args.outBaseName, args.outDirName)
# debugging info
logfile = args.outDirName + "/" + args.outBaseName + "/logs/%d" % os.getpid(
) + "." + args.outBaseName + ".peakparser.log"
logging.basicConfig(format='%(asctime)s %(message)s',
filename=logfile,
level=logging.DEBUG)
# log parameters
logging.info("\noutBaseName=%s\nbamFileName=%s\nexonTabixFile=%s" %
(args.outBaseName, configDict['readFileName'],
configDict['exonTabixFile']))
pickreads.checkfile(configDict['readFileName'])
pickreads.checkfile(configDict['exonTabixFile'])
pickreads.checkfile(args.pgTabixFile)
tabixFile = pysam.Tabixfile(configDict['exonTabixFile'], 'r')
pgTabix = pysam.Tabixfile(args.pgTabixFile, 'r')
pgTabixContigs = {}
for contig in pgTabix.contigs:
pgTabixContigs[contig] = 1
# structure for keeping element classes seperate
geneNameDict = {}
f = open(configDict['readFileName'])
for line in f:
fields = line.rsplit("\t")
chrom = fields[0]
readPos = int(fields[1])
readStrand = fields[2]
mateElt = fields[3]
mateChrom = fields[4]
mateStrand = fields[5]
matePos = int(fields[6])
eltStart = int(fields[7])
eltEnd = int(fields[8])
eltStrand = fields[9]
eltFullLen = int(fields[10])
genomeName = fields[11]
peakIndex = fields[12]
geneName = fields[13].strip()
if not geneNameDict.has_key(geneName):
geneNameDict[geneName] = PeakBuilder(geneName)
pair = pairinfo.Pair(chrom, readPos, readStrand, mateElt, mateChrom,
mateStrand, matePos, eltStart, eltEnd, eltStrand,
eltFullLen, genomeName, peakIndex, geneName)
if geneNameDict[geneName].lastPeakNum != peakIndex:
geneNameDict[geneName].peaks.append(geneNameDict[geneName].peak)
geneNameDict[geneName].peak = pairinfo.Peak()
geneNameDict[geneName].peak.addpair(pair)
geneNameDict[geneName].lastPeakNum = peakIndex
else:
geneNameDict[geneName].peak.addpair(pair)
for geneName in geneNameDict.keys():
geneNameDict[geneName].peaks.append(geneNameDict[geneName].peak)
logging.info("starting long output...")
longOutput(geneNameDict, args.outBaseName, args.outDirName, pgTabix,
pgTabixContigs)
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):
checkOutDir(args.outBaseName,args.outDirName)
configPath = args.outDirName + "/" + args.outBaseName + "/" + args.configFileName
pickreads.checkfile(configPath)
configDict = readConfig(configPath,args.outBaseName,args.outDirName)
# debugging info
logfile = args.outDirName + "/" + args.outBaseName + "/logs/%d" % os.getpid() + "." + args.outBaseName +".peakparser.log"
logging.basicConfig(format='%(asctime)s %(message)s',filename=logfile,level=logging.DEBUG)
# log parameters
logging.info("\noutBaseName=%s\nbamFileName=%s\nexonTabixFile=%s"
% (args.outBaseName,configDict['readFileName'],configDict['exonTabixFile']))
pickreads.checkfile(configDict['readFileName'])
pickreads.checkfile(configDict['exonTabixFile'])
pickreads.checkfile(args.pgTabixFile)
tabixFile = pysam.Tabixfile(configDict['exonTabixFile'], 'r')
pgTabix = pysam.Tabixfile(args.pgTabixFile, 'r')
pgTabixContigs = {}
for contig in pgTabix.contigs:
pgTabixContigs[contig] = 1
# structure for keeping element classes seperate
geneNameDict = {}
f = open(configDict['readFileName'])
for line in f:
fields = line.rsplit("\t")
chrom = fields[0]
readPos = int(fields[1])
readStrand = fields[2]
mateElt = fields[3]
mateChrom = fields[4]
mateStrand = fields[5]
matePos = int(fields[6])
eltStart = int(fields[7])
eltEnd = int(fields[8])
eltStrand = fields[9]
eltFullLen = int(fields[10])
genomeName = fields[11]
peakIndex = fields[12]
geneName = fields[13].strip()
if not geneNameDict.has_key(geneName):
geneNameDict[geneName] = PeakBuilder(geneName);
pair = pairinfo.Pair(chrom,readPos,readStrand,mateElt,mateChrom,
mateStrand,matePos,eltStart,eltEnd,eltStrand,
eltFullLen,genomeName,peakIndex,geneName)
if geneNameDict[geneName].lastPeakNum != peakIndex:
geneNameDict[geneName].peaks.append(geneNameDict[geneName].peak)
geneNameDict[geneName].peak = pairinfo.Peak()
geneNameDict[geneName].peak.addpair(pair)
geneNameDict[geneName].lastPeakNum = peakIndex
else:
geneNameDict[geneName].peak.addpair(pair)
for geneName in geneNameDict.keys():
geneNameDict[geneName].peaks.append(geneNameDict[geneName].peak)
logging.info("starting long output...")
longOutput(geneNameDict,args.outBaseName,args.outDirName,pgTabix,pgTabixContigs)