def createMTrack(dirName): '''merge all mapped tracks in directory and create a single wig file''' fileList = cg.recurseDir(dirName, end = '.out') chroms = cg.humanChromosomes print 'Making Bed File vectors' cvg = HTSeq.GenomicArray(chroms, stranded=True, typecode='i') for fName in fileList: print fName alignment_file = HTSeq.BowtieReader(fName) for alngt in alignment_file: if alngt.aligned: try: cvg.add_value( 1, alngt.iv ) #iv is the genomic interval.. except KeyError: pass bedNamePos = dirName + '/Merge.' + 'hg19' + '.1.wig' bedNameNeg = dirName + '/Merge.' + 'hg19' + '.-1.wig' print 'Writing Bed File' cvg.write_bedgraph_file(bedNamePos, "+" ) cvg.write_bedgraph_file(bedNameNeg, "-" ) #Now extend it updateWigLength(bedNamePos, 'hg19') updateWigLength(bedNameNeg, 'hg19') #Now Sort it. cgSort.wigSort(bedNamePos) cgSort.wigSort(bedNameNeg)
def createTrack(fName, organism): if organism == 'human': chroms = cg.humanChromosomes assembly = 'hg19' elif organism == 'mouse': chroms = cg.mouseChromosomes assembly = 'mm9' elif organism == 'zebrafish': chroms = cg.zebrafishChromosomes assembly = 'danRer6' alignment_file = HTSeq.BowtieReader(fName) cvg = HTSeq.GenomicArray(chroms, stranded=True, typecode='i') for alngt in alignment_file: if alngt.aligned: cvg.add_value( 1, alngt.iv ) #iv is the genomic interval.. bedNamePos = fName + '.1.' + 'wig' bedNameNeg = fName + '.-1.' + 'wig' cvg.write_bedgraph_file(bedNamePos, "+" ) cvg.write_bedgraph_file(bedNameNeg, "-" ) #Now extend it and sort it. updateWigLength(bedNamePos, assembly) updateWigLength(bedNameNeg, assembly) #Now Sort it. cgSort.wigSort(bedNamePos) cgSort.wigSort(bedNameNeg)
def createMultiTrackDir(dirName, organism):
'''THIS DIFFERS FROM ABOVE BECAUSE IT DOESN't REQUIRE META INFO
IT JUST MAKES A MERGED WIG FOR EVERYTHING IN THE DIRECTORY'''
mainConf = c.cgConfig('Main.conf')
fileList = []
for file in cg.recurseDir(dirName, end = '.mapped'):
fileList.append(file)
#make merged wig
if organism == 'human':
chroms = cg.humanChromosomes
assembly = 'hg19'
elif organism == 'mouse':
chroms = cg.mouseChromosomes
assembly = 'mm9'
elif organism == 'zebrafish':
chroms = cg.zebrafishChromosomes
assembly = 'danRer6'
print 'Making Bed File vectors'
cvg = HTSeq.GenomicArray(chroms, stranded=True, typecode='i')
for fName in fileList:
alignment_file = HTSeq.BowtieReader(fName)
for alngt in alignment_file:
if alngt.aligned:
cvg.add_value( 1, alngt.iv ) #iv is the genomic interval..
bedNamePos = dirName + '/Merge.' + organism + '.1.wig'
bedNameNeg = dirName + '/Merge.' + organism + '.-1.wig'
print 'Writing Bed File'
cvg.write_bedgraph_file(bedNamePos, "+" )
cvg.write_bedgraph_file(bedNameNeg, "-" )
#Now extend it
updateWigLength(bedNamePos, assembly)
updateWigLength(bedNameNeg, assembly)
#Now Sort it.
cgSort.wigSort(bedNamePos)
cgSort.wigSort(bedNameNeg)
import cgConfig as c
import bioLibCG as cg
import cgSort
mConf = c.cgConfig('Main.conf')
smallPath = mConf.conf['smallPath']
smallPath = '/home/chrisgre/smallLibs/WIGS/zebrafish'
#grab everything - NOT WIG MERGES...
smallLibs = cg.recurseDir(smallPath, end = '.wig')
smallLibs.extend(cg.recurseDir(smallPath, end = '.wig'))
for lib in smallLibs:
print 'sorting', lib
cgSort.wigSort(lib)
def createMultiTrack(dirName, organism):
'''merge all mapped tracks in directory and create a single wig file'''
mainConf = c.cgConfig('Main.conf')
metaFileName = mainConf.conf['metaFileName']
fileList = []
for file in cg.recurseDir(dirName, end = '.mapped'):
#check if mouse or human SHOULD PUT INTO A STD FUNCTION FOR META FILE
#check if mouse or human
baseFName = cg.getBaseFileName(file, naked= True)
metaDict = cg.getMetaFileDict(metaFileName)
org = 'None'
if baseFName in metaDict:
if metaDict[baseFName][1] == 'NONE':
print ' NO ORG KNOWN FOR', file
continue
elif not metaDict[baseFName][1] == organism:
print ' NOT ORGANISM RUNNING', file
continue
else:
org = metaDict[baseFName][1]
print ' USING ORG', org, file
#check if there is an organism, must check due to files not in metaFile
if org == 'None':
print ' NO org (not in meta file)', file
continue
#only make wig file for organism asked for
if not org == organism:
continue
#if it is right organism and has mapped file then add
fileList.append(file)
#make merged wig
if organism == 'human':
chroms = cg.humanChromosomes
assembly = 'hg19'
elif organism == 'mouse':
chroms = cg.mouseChromosomes
assembly = 'mm9'
elif organism == 'zebrafish':
chroms = cg.zebrafishChromosomes
assembly = 'danRer6'
print 'Making Bed File vectors'
cvg = HTSeq.GenomicArray(chroms, stranded=True, typecode='i')
for fName in fileList:
alignment_file = HTSeq.BowtieReader(fName)
for alngt in alignment_file:
if alngt.aligned:
cvg.add_value( 1, alngt.iv ) #iv is the genomic interval..
bedNamePos = dirName + '/Merge.' + organism + '.1.wig'
bedNameNeg = dirName + '/Merge.' + organism + '.-1.wig'
print 'Writing Bed File'
cvg.write_bedgraph_file(bedNamePos, "+" )
cvg.write_bedgraph_file(bedNameNeg, "-" )
#Now extend it
updateWigLength(bedNamePos, assembly)
updateWigLength(bedNameNeg, assembly)
#Now Sort it.
cgSort.wigSort(bedNamePos)
cgSort.wigSort(bedNameNeg)