def mapFastQ(fName, organism): indexFileHuman = '/home/chrisgre/indexes/bowtie/hg19' indexFileMouse = '/home/chrisgre/indexes/bowtie/mm9' indexFileZebrafish = '/home/chrisgre/indexes/bowtie/danRer6' if organism == 'human': indexName = indexFileHuman elif organism == 'mouse': indexName = indexFileMouse elif organism == 'zebrafish': indexName = indexFileZebrafish outName = fName + '.mapped' logFile = open(mainConf.conf['outLog'] + cg.getBaseFileName(fName), 'w') errorFile = open(mainConf.conf['errorLog'] + cg.getBaseFileName(fName), 'w') if fastQTypes.getFastQType(fName, quick = True) == 'Sa': print 'Mapping with 33 phred offset' subprocess.Popen(['bowtie', '--phred33-quals', '-k', '20', '-m', '20', '-p', '1', indexName, fName, outName], stdout=logFile, stderr=errorFile).wait() else: print 'Mapping with 64 phred offset' subprocess.Popen(['bowtie', '--phred64-quals', '-k', '20', '-m', '20', '-p', '1', indexName, fName, outName], stdout=logFile, stderr=errorFile).wait() logFile.close() errorFile.close()
def testmerge(masterDir, parDir):
'''The master directory will contain the merged objects,
the slave directory contains the directories of all the runs
oRNA (master)
aDir (master)
pRuns
--run.00
----oRNA (slave: pRuns/run.00/oRNA)
----aDir
--run.01
'''
mDC = cgDB.dataController(masterDir, cgAlignment.cgAlignment)
id_masterObj = mDC.load()
#recurse through all the runs
masterBN = bioLibCG.getBaseFileName(masterDir)
for slaveDir in bioLibCG.recursePaths(parDir, end = masterBN):
oDC = cgDB.dataController(slaveDir, cgAlignment.cgAlignment)
id_slaveObj = oDC.load()
id_masterObj = cgDB.mergeTwoObjects(id_masterObj, id_slaveObj, cgOriginRNA.OriginRNA)
mDC.commit(id_masterObj)
def makeWig(fN, assembly, format=None, name=None):
'''format assumes bowtie
suitible for medium mapped files.
takes longer.'''
#assume bowtie
if not format: format = 'Bowtie'
parserFunction = returnParserFunction(format)
if not name: name = cg.getBaseFileName(fN, naked=True)
lDict = cg.returnChromLengthDict(assembly)
for chrom in lDict:
if not chrom in cg.acceptableChroms: continue
for strand in ['1', '-1']:
f = open(fN, 'r')
#create hitmap of chrom and strand
print chrom, strand, 'hitmap'
hitDict = {}
for line in f:
lChrom, lStrand, start, end = cg.tccSplit(parserFunction(line))
lStrand = str(lStrand)
start = int(start)
end = int(end)
if chrom == lChrom and strand == lStrand:
for i in range(start, end + 1):
try:
hitDict[i] += 1
except KeyError:
hitDict[i] = 1
#write results to wig file
writeWigFromHitDict(hitDict, assembly)
def testmerge(masterDir, parDir):
'''The master directory will contain the merged objects,
the slave directory contains the directories of all the runs
oRNA (master)
aDir (master)
pRuns
--run.00
----oRNA (slave: pRuns/run.00/oRNA)
----aDir
--run.01
'''
mDC = cgDB.dataController(masterDir, cgAlignment.cgAlignment)
id_masterObj = mDC.load()
#recurse through all the runs
masterBN = bioLibCG.getBaseFileName(masterDir)
for slaveDir in bioLibCG.recursePaths(parDir, end=masterBN):
oDC = cgDB.dataController(slaveDir, cgAlignment.cgAlignment)
id_slaveObj = oDC.load()
id_masterObj = cgDB.mergeTwoObjects(id_masterObj, id_slaveObj,
cgOriginRNA.OriginRNA)
mDC.commit(id_masterObj)
def makeWig(fN, assembly, format = None, name = None):
'''format assumes bowtie
suitible for medium mapped files.
takes longer.'''
#assume bowtie
if not format: format = 'Bowtie'
parserFunction = returnParserFunction(format)
if not name: name = cg.getBaseFileName(fN, naked = True)
lDict = cg.returnChromLengthDict(assembly)
for chrom in lDict:
if not chrom in cg.acceptableChroms: continue
for strand in ['1', '-1']:
f = open(fN, 'r')
#create hitmap of chrom and strand
print chrom, strand, 'hitmap'
hitDict = {}
for line in f:
lChrom, lStrand, start, end = cg.tccSplit(parserFunction(line))
lStrand = str(lStrand)
start = int(start)
end = int(end)
if chrom == lChrom and strand == lStrand:
for i in range(start, end + 1):
try:
hitDict[i] += 1
except KeyError:
hitDict[i] = 1
#write results to wig file
writeWigFromHitDict(hitDict, assembly)
def writeWigFromHitDict(hitDict, assembly, name, directory=None):
mConf = c.getConfig('Main.conf')
if not directory: directory = mConf.conf['wigs']
if not name: name = cg.getBaseFileName(name, naked=True)
lDict = cg.returnChromLengthDict(assembly)
cg.clearDirectory(directory, overwrite=False)
#write results to wig file
for chrom in hitDict:
for strand in hitDict[chrom]:
oF = open(directory + '/%s.%s.%s.wig' % (name, chrom, strand), 'w')
oF.write('track type=bedGraph name=%s.%s.%s\n' %
(name, chrom, strand))
#print ' sorting'
#print hitDict[chrom]
chromEnd = lDict[chrom] #
hitDict[chrom][strand][chromEnd] = 0
keys = hitDict[chrom][strand].keys()
keys.sort()
#print ' writing blocks'
prevVal = 0
prevCoord = 0
blockStart = 0
blockEnd = 1
for key in keys:
val = hitDict[chrom][strand][key]
if prevCoord == key - 1:
if val == prevVal: #should be combined
blockEnd = key + 1
else: #no zero block
#write old block
oF.write('%s\t%s\t%s\t%s\n' %
(chrom, blockStart, blockEnd,
prevVal)) #!make it a float value?
#start new block
blockStart = key
blockEnd = key + 1
else:
#write old block
oF.write('%s\t%s\t%s\t%s\n' %
(chrom, blockStart, blockEnd, prevVal))
#write zero block
oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockEnd, key, 0))
#start new block
blockStart = key
blockEnd = key + 1
prevVal = val
prevCoord = key
oF.close()
def mixWig(directory, assembly, name=None):
'''Does it by chromosome --> faster, less memory'''
if not name: name = 'Merge'
#gather all chromosomes
chromList = []
for fN in cg.recurseDir(directory, end='.wig'):
chrom = cg.getBaseFileName(fN).strip().split('.')[-3]
if chrom not in chromList:
chromList.append(chrom)
print chromList
for chrom in chromList:
print chrom
#Gather all the values from all the files
hitDict = {} # chrom : { strand : coord
for fN in cg.recurseDir(directory, end='.wig'):
fChrom = cg.getBaseFileName(fN).strip().split('.')[-3]
if fChrom != chrom: continue
print ' ', fN, fChrom
f = open(fN, 'r')
f.readline() #header
strand = cg.getBaseFileName(fN).strip().split('.')[-2]
for line in f:
lChrom, start, end, val = (line.strip().split('\t'))
start, end, val = int(start), int(end), int(val)
if val < 1: continue
#print start, end, val
for i in range(start, end):
try:
hitDict[lChrom][strand][i] += val
except (KeyError, TypeError):
if not lChrom in hitDict:
hitDict[lChrom] = {}
if not strand in hitDict[lChrom]:
hitDict[lChrom][strand] = {}
hitDict[lChrom][strand][i] = val
#write results to wig file
writeWigFromHitDict(hitDict, assembly, name, directory)
def mixWig(directory, assembly, name = None):
'''Does it by chromosome --> faster, less memory'''
if not name: name = 'Merge'
#gather all chromosomes
chromList = []
for fN in cg.recurseDir(directory, end = '.wig'):
chrom = cg.getBaseFileName(fN).strip().split('.')[-3]
if chrom not in chromList:
chromList.append(chrom)
print chromList
for chrom in chromList:
print chrom
#Gather all the values from all the files
hitDict = {} # chrom : { strand : coord
for fN in cg.recurseDir(directory, end = '.wig'):
fChrom = cg.getBaseFileName(fN).strip().split('.')[-3]
if fChrom != chrom: continue
print ' ', fN, fChrom
f = open(fN, 'r')
f.readline() #header
strand = cg.getBaseFileName(fN).strip().split('.')[-2]
for line in f:
lChrom, start, end, val = (line.strip().split('\t'))
start, end, val = int(start), int(end), int(val)
if val < 1: continue
#print start, end, val
for i in range(start, end):
try:
hitDict[lChrom][strand][i] += val
except (KeyError,TypeError):
if not lChrom in hitDict:
hitDict[lChrom] = {}
if not strand in hitDict[lChrom]:
hitDict[lChrom][strand] = {}
hitDict[lChrom][strand][i] = val
#write results to wig file
writeWigFromHitDict(hitDict, assembly, name, directory)
def makeWigMem(fN, assembly, format = None, name = None, directory = None):
'''format assumes bowtie
suitible for small mapped files.'''
if not name: name = cg.getBaseFileName(fN, naked = True)
if not format: format = 'Bowtie'
parserFunction = returnParserFunction(format)
lDict = cg.returnChromLengthDict(assembly)
f = open(fN, 'r')
f.readline() #header...file might not have one but its one read...
#create hitmap of chrom and strand
hitDict = {} #format = chr: { strand : { coord : value
for line in f:
try:
lChrom, lStrand, start, end = cg.tccSplit(parserFunction(line))
except AttributeError:
continue
lStrand = str(lStrand)
start = int(start)
end = int(end)
if lChrom in cg.acceptableChroms:
#wig for degradome
if lStrand == '1':
i = start + 20
else:
i = start
try:
hitDict[lChrom][lStrand][i] += 1
except KeyError:
if lChrom not in hitDict:
hitDict[lChrom] = {}
if lStrand not in hitDict[lChrom]:
hitDict[lChrom][lStrand] = {}
hitDict[lChrom][lStrand][i] = 1
'''
for i in range(start, end):
try:
hitDict[lChrom][lStrand][i] += 1
except KeyError:
if lChrom not in hitDict:
hitDict[lChrom] = {}
if lStrand not in hitDict[lChrom]:
hitDict[lChrom][lStrand] = {}
hitDict[lChrom][lStrand][i] = 1
'''
f.close()
#write results to wig file
writeWigFromHitDict(hitDict, assembly, name, directory)
def makeWigMem(fN, assembly, format=None, name=None, directory=None):
'''format assumes bowtie
suitible for small mapped files.'''
if not name: name = cg.getBaseFileName(fN, naked=True)
if not format: format = 'Bowtie'
parserFunction = returnParserFunction(format)
lDict = cg.returnChromLengthDict(assembly)
f = open(fN, 'r')
f.readline() #header...file might not have one but its one read...
#create hitmap of chrom and strand
hitDict = {} #format = chr: { strand : { coord : value
for line in f:
try:
lChrom, lStrand, start, end = cg.tccSplit(parserFunction(line))
except AttributeError:
continue
lStrand = str(lStrand)
start = int(start)
end = int(end)
if lChrom in cg.acceptableChroms:
#wig for degradome
if lStrand == '1':
i = start + 20
else:
i = start
try:
hitDict[lChrom][lStrand][i] += 1
except KeyError:
if lChrom not in hitDict:
hitDict[lChrom] = {}
if lStrand not in hitDict[lChrom]:
hitDict[lChrom][lStrand] = {}
hitDict[lChrom][lStrand][i] = 1
'''
for i in range(start, end):
try:
hitDict[lChrom][lStrand][i] += 1
except KeyError:
if lChrom not in hitDict:
hitDict[lChrom] = {}
if lStrand not in hitDict[lChrom]:
hitDict[lChrom][lStrand] = {}
hitDict[lChrom][lStrand][i] = 1
'''
f.close()
#write results to wig file
writeWigFromHitDict(hitDict, assembly, name, directory)
def writeWigFromHitDict(hitDict, assembly, name, directory = None):
mConf = c.getConfig('Main.conf')
if not directory: directory = mConf.conf['wigs']
if not name: name = cg.getBaseFileName(name, naked = True)
lDict = cg.returnChromLengthDict(assembly)
cg.clearDirectory(directory, overwrite = False)
#write results to wig file
for chrom in hitDict:
for strand in hitDict[chrom]:
oF = open(directory + '/%s.%s.%s.wig' % (name, chrom, strand), 'w')
oF.write('track type=bedGraph name=%s.%s.%s\n' % (name, chrom, strand))
#print ' sorting'
#print hitDict[chrom]
chromEnd = lDict[chrom] #
hitDict[chrom][strand][chromEnd] = 0
keys = hitDict[chrom][strand].keys()
keys.sort()
#print ' writing blocks'
prevVal = 0
prevCoord = 0
blockStart = 0
blockEnd = 1
for key in keys:
val = hitDict[chrom][strand][key]
if prevCoord == key - 1:
if val == prevVal:#should be combined
blockEnd = key + 1
else: #no zero block
#write old block
oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockStart, blockEnd, prevVal)) #!make it a float value?
#start new block
blockStart = key
blockEnd = key + 1
else:
#write old block
oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockStart, blockEnd, prevVal))
#write zero block
oF.write('%s\t%s\t%s\t%s\n' % (chrom, blockEnd, key, 0))
#start new block
blockStart = key
blockEnd = key + 1
prevVal = val
prevCoord = key
oF.close()
def clipAdapter(fName, adapter = None, validate = False, oName = None, overwrite = True):
#Check to see if the file exists:
putativeN = fName.replace('.fastq','.clipped.fastq')
if os.path.isfile(putativeN):
if overwrite:
print ' Overwriting file', putativeN
os.remove(putativeN)
else:
print ' \nNOT OVERWRITING FILE', putativeN
return 1
#If the adapter is none, try to find it in the small.meta file
if adapter is None:
baseFName = cg.getBaseFileName(fName) + '.counts'
for metaFileName in metaFileNames:
mFile = open(metaFileName, 'r')
for line in mFile:
fields = line.strip().split('\t')
if baseFName == fields[0]:
if fields[3] == 'NONE':
print ' NO ADAPTER KNOWN FOR', fName
return 1
else:
adapter = fields[3]
print ' Using adapter', adapter, fName
mFile.close()
#Is it a valid fastq file?
if validate:
pass
#check the type of fastq file
sangerType = False
fType = fastQTypes.getFastQType(fName, quick = True)
if fType == 'Sa':
sangerType = True
print ' Detected format:', fType, fName
#Run it through clipper
print 'Clipping file', fName
if oName is None:
oName = fName.replace('.fastq','.clipped.fastq')
if sangerType:
subprocess.Popen(['fastx_clipper', '-n', '-v', '-Q', '33', '-i', str(fName), '-a', str(adapter), '-o', str(oName)]).wait()
else:
subprocess.Popen(['fastx_clipper', '-n', '-v', '-i', str(fName), '-a', str(adapter), '-o', str(oName)]).wait()
print ' DONE', fName
def clipAdapter(fName, adapter=None, validate=False, oName=None):
#If the adapter is none, try to find it in the small.meta file
if adapter is None:
baseFName = cg.getBaseFileName(fName) + '.counts'
for metaFileName in metaFileNames:
mFile = open(metaFileName, 'r')
for line in mFile:
fields = line.strip().split('\t')
if baseFName == fields[0]:
if fields[3] == 'NONE':
print 'NO ADAPTER KNOWN FOR', fName
return 1
else:
adapter = fields[3]
print 'Using adapter', adapter
mFile.close()
#Is it a valid fastq file?
if validate:
pass
#check the type of fastq file
sangerType = False
fType = fastQTypes.getFastQType(fName, quick=True)
if fType == 'Sa':
sangerType = True
print 'Detected format:', fType
#Run it through clipper
print 'Clipping file'
if oName is None:
oName = fName.replace('.fastq', '.clipped.fastq')
if sangerType:
subprocess.Popen([
'fastx_clipper', '-v', '-Q', '33', '-i',
str(fName), '-a',
str(adapter), '-o',
str(oName)
]).wait()
else:
subprocess.Popen([
'fastx_clipper', '-v', '-i',
str(fName), '-a',
str(adapter), '-o',
str(oName)
]).wait()
print 'DONE'
def plotResults(fN, cName=None):
cHairs = getHairpins.getHairpins(fN) #CID: HAIRPIN
directory = cg.getBaseFileName(fN)
cg.clearDirectory(directory)
#change the directory before plotting
cwd = os.getcwd()
os.chdir(directory)
for CID in cHairs:
print 'plotting:', CID
cgPlot.plotASProfile(cHairs[CID], cName)
os.chdir(cwd)
def plotResults(fN, cName = None): cHairs = getHairpins.getHairpins(fN) #CID: HAIRPIN directory = cg.getBaseFileName(fN) cg.clearDirectory(directory) #change the directory before plotting cwd = os.getcwd() os.chdir(directory) for CID in cHairs: print 'plotting:', CID cgPlot.plotASProfile(cHairs[CID], cName) os.chdir(cwd)
def mapFastQInDirQ(dirName, overwrite = True):
'''Every Q function has a corresponding shell script'''
wrapperShell = '/home/chrisgre/scripts/mapping/mapFastQ.sh'
for file in cg.recurseDir(dirName, end = 'clipped.fastq'):
print file
putativeN = file.replace('.clipped.fastq','.clipped.fastq.mapped')
if os.path.isfile(putativeN):
if overwrite:
print ' Overwriting file', putativeN
os.remove(putativeN)
else:
print ' \nNOT OVERWRITING FILE', putativeN
continue
#check if mouse or human
baseFName = cg.getBaseFileName(file, naked = True)
org = 'None'
for metaFileName in metaFileNames:
mFile = open(metaFileName, 'r')
for line in mFile:
fields = line.strip().split('\t')
if baseFName == fields[0]:
if fields[2] == 'NONE':
print ' NO ORG KNOWN FOR', file
continue
else:
org = fields[2]
print ' USING ORG', org, file
mFile.close()
#check if there is an organism, must check due to files not in metaFile
if org == 'None':
print ' NO org', file
continue
while True:
#submit job if there are less than ten
if clusterCheck.queryNumJobsQ('chrisgre') < 40:
#subprocess.Popen(['qsub', '-q', 'xiao', '-l', 'mem=4G', '-V', '-o', mainConf.conf['outLog'], '-e', mainConf.conf['errorLog'], wrapperShell, file, org ])
subprocess.Popen(['qsub', '-l', 'mem=4G', '-V', '-o', mainConf.conf['outLog'], '-e', mainConf.conf['errorLog'], wrapperShell, file, org ])
time.sleep(.2) #give it time to update qstat
break
else:#wait 10 secs...
time.sleep(20)
def createTrackInDir(dirName):
'''Every Q function has a corresponding shell script
Make wig file for all mapped files, for all organisms'''
wrapperShell = '/home/chrisgre/scripts/mapping/createTrack.sh'
mainConf = c.cgConfig('Main.conf')
metaFileName = mainConf.conf['metaFileName']
for file in cg.recurseDir(dirName, end = '.mapped'):
#check if mouse or human
baseFName = cg.getBaseFileName(file)
baseFName = baseFName.split('.')[0]
metaDict = cg.getMetaFileDict(metaFileName)
org = 'None'
if baseFName in metaDict:
if metaDict[baseFName][1] == 'NONE':
print ' NO ORG KNOWN FOR', 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
while True:
#submit job if there are less than ten
if clusterCheck.queryNumJobsQ('chrisgre') < 1000:
#subprocess.Popen(['qsub', '-q', 'xiao', '-l', 'mem=4G', '-V', '-o', mainConf.conf['outLog'], '-e', mainConf.conf['errorLog'], wrapperShell, file, org ])
subprocess.Popen(['qsub', '-V', '-o', mainConf.conf['outLog'], '-e', mainConf.conf['errorLog'], wrapperShell, file, org ])
#time.sleep(.5) #give it time to update qstat
break
else:#wait 10 secs...
time.sleep(20)
def makeWigMem(fN, assembly, format = None, name = None, directory = None, degWig = False, switchStrand = True, normalized = False):
'''format assumes bowtie
suitible for small mapped files.
switch strand does not switch the strands, it just makes sure if the data is backwards (HeLa) that it will
put the peak in the right spot'''
print 'degWig Value', degWig
print 'switch strands?', switchStrand
if not name: name = cg.getBaseFileName(fN, naked = True)
if not format: format = 'Bowtie'
parserFunction = returnParserFunction(format)
lDict = cg.returnChromLengthDict(assembly)
f = open(fN, 'r')
f.readline() #header...file might not have one but its one read...
#create hitmap of chrom and strand
hitDict = {} #format = chr: { strand : { coord : value
for line in f:
lChrom, lStrand, start, end = cg.tccSplit(parserFunction(line))
lStrand = str(lStrand)
start = int(start)
end = int(end)
numPlacesMapped = int(line.strip().split('\t')[6])
numPlacesMapped += 1
readCount = 1
if normalized:
readCount = float(readCount)/numPlacesMapped
if lChrom in cg.acceptableChroms:
if degWig:
#wig for degradome NOTE:!!! change lStrand == '1' to '-1' for Bracken!
if switchStrand:
if lStrand == '1':
i = start + (end - start)
else:
i = start + 1
else:
if lStrand == '-1':
i = start + (end - start)
else:
i = start + 1
hitDict.setdefault(lChrom, {}).setdefault(lStrand, {})
hitDict[lChrom][lStrand][i] = hitDict[lChrom][lStrand].get(i, 0) + readCount
else:
#wig for regular
for i in range(start, end):
try:
hitDict[lChrom][lStrand][i] += readCount
except KeyError:
if lChrom not in hitDict:
hitDict[lChrom] = {}
if lStrand not in hitDict[lChrom]:
hitDict[lChrom][lStrand] = {}
hitDict[lChrom][lStrand][i] = readCount
f.close()
#write results to wig file
writeWigFromHitDict(hitDict, assembly, name, directory)
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)
#make lib:hits dict
densityFile = open('/home/chrisgre/scripts/readDensity/individual.densities.data', 'r')
tissueHits = {}
cID = 'NONE'
for line in densityFile:
if line.startswith('\t'): #lib: hit
l = line.strip().split('\t')[0]
hits = int(line.strip().split('\t')[1])
tissueHits[cID][l] = hits
else:
cID = line.strip()
tissueHits[cID] = {}
tissueHist = {}#tissue: hits
for mirID in mirIDs:
if mirID in tissueHits:
for smallLib in tissueHits[mirID]:
smallName = cg.getBaseFileName(smallLib, naked = True)
if smallName in metaDict:
if metaDict[smallName][1] == 'mouse':
if len(metaDict[smallName]) > 3:
t = metaDict[smallName][3]
if t in tissueHist:
tissueHist[t] += tissueHits[mirID][smallLib]
else:
tissueHist[t] = tissueHits[mirID][smallLib]
print tissueHist
direc = '/home/chrisgre/apps/projects/small.rna.libs'
metaFileName = direc + '/' + 'small.meta'
##make data of already made file so there aren't any duplicates:
fileDict = {} #filename...
metaFile = open(metaFileName, 'r')
#add new entries
countFiles = cg.recurseDir(direc, end='.fastq')
for file in countFiles:
fileName = file.strip().split('/')[-1]
if len(fileName.split('.')) > 2: #has to specifically end in fastq...
continue
fileName = cg.getBaseFileName(file, naked=True)
dir = file.strip().split('/')[-2]
org = 'NONE'
if 'human' in dir:
org = 'human'
if 'mouse' in dir:
org = 'mouse'
if 'pig' in dir:
org = 'pig'
if 'dog' in dir:
org = 'dog'
if 'rat' in dir:
org = 'rat'
if 'zebrafish' in dir:
org = 'zebrafish'
if metaDict[baseFName][1] == organism:
organismFileList.append(baseFName)
#put small hits for each prediction in dictionary
pCount = {}
smallFile = open(smallFileName, 'r')
currID = 'NONE'
for line in smallFile:
if '\t' not in line: #This is the line with the id in it --> store another ID
currID = line.strip()
else: #this line contains library and count info --> add
lib = line.strip().split('\t')[0]
count = int(line.strip().split('\t')[1])
if cg.getBaseFileName(lib, naked=True) in organismFileList:
if currID in pCount:
pCount[currID] = pCount[currID] + count
else:
pCount[currID] = count
#update the file --> any line with kmer on it give it the count
newLines = []
predFile = open(pFileName, 'r')
for line in predFile:
kmer = line.strip().split('\t')[0].split('.')[0]
if kmer in pCount:
numSmall = pCount[kmer]
else:
numSmall = 0
newLine = line.strip().split('\t')
#make lib:hits dict
densityFile = open(
'/home/chrisgre/scripts/readDensity/individual.densities.data', 'r')
tissueHits = {}
cID = 'NONE'
for line in densityFile:
if line.startswith('\t'): #lib: hit
l = line.strip().split('\t')[0]
hits = int(line.strip().split('\t')[1])
tissueHits[cID][l] = hits
else:
cID = line.strip()
tissueHits[cID] = {}
tissueHist = {} #tissue: hits
for mirID in mirIDs:
if mirID in tissueHits:
for smallLib in tissueHits[mirID]:
smallName = cg.getBaseFileName(smallLib, naked=True)
if smallName in metaDict:
if metaDict[smallName][1] == 'mouse':
if len(metaDict[smallName]) > 3:
t = metaDict[smallName][3]
if t in tissueHist:
tissueHist[t] += tissueHits[mirID][smallLib]
else:
tissueHist[t] = tissueHits[mirID][smallLib]
print tissueHist
def makeWigMem(fN,
assembly,
format=None,
name=None,
directory=None,
degWig=False,
switchStrand=True,
normalized=False):
'''format assumes bowtie
suitible for small mapped files.
switch strand does not switch the strands, it just makes sure if the data is backwards (HeLa) that it will
put the peak in the right spot'''
print 'degWig Value', degWig
print 'switch strands?', switchStrand
if not name: name = cg.getBaseFileName(fN, naked=True)
if not format: format = 'Bowtie'
parserFunction = returnParserFunction(format)
lDict = cg.returnChromLengthDict(assembly)
f = open(fN, 'r')
f.readline() #header...file might not have one but its one read...
#create hitmap of chrom and strand
hitDict = {} #format = chr: { strand : { coord : value
for line in f:
lChrom, lStrand, start, end = cg.tccSplit(parserFunction(line))
lStrand = str(lStrand)
start = int(start)
end = int(end)
numPlacesMapped = int(line.strip().split('\t')[6])
numPlacesMapped += 1
readCount = 1
if normalized:
readCount = float(readCount) / numPlacesMapped
if lChrom in cg.acceptableChroms:
if degWig:
#wig for degradome NOTE:!!! change lStrand == '1' to '-1' for Bracken!
if switchStrand:
if lStrand == '1':
i = start + (end - start)
else:
i = start + 1
else:
if lStrand == '-1':
i = start + (end - start)
else:
i = start + 1
hitDict.setdefault(lChrom, {}).setdefault(lStrand, {})
hitDict[lChrom][lStrand][i] = hitDict[lChrom][lStrand].get(
i, 0) + readCount
else:
#wig for regular
for i in range(start, end):
try:
hitDict[lChrom][lStrand][i] += readCount
except KeyError:
if lChrom not in hitDict:
hitDict[lChrom] = {}
if lStrand not in hitDict[lChrom]:
hitDict[lChrom][lStrand] = {}
hitDict[lChrom][lStrand][i] = readCount
f.close()
#write results to wig file
writeWigFromHitDict(hitDict, assembly, name, directory)
direc = '/home/chrisgre/apps/projects/small.rna.libs'
metaFileName = direc + '/' + 'small.meta'
##make data of already made file so there aren't any duplicates:
fileDict = {} #filename...
metaFile = open(metaFileName, 'r')
#add new entries
countFiles = cg.recurseDir(direc, end = '.fastq')
for file in countFiles:
fileName = file.strip().split('/')[-1]
if len(fileName.split('.')) > 2: #has to specifically end in fastq...
continue
fileName = cg.getBaseFileName(file, naked = True)
dir = file.strip().split('/')[-2]
org = 'NONE'
if 'human' in dir:
org = 'human'
if 'mouse' in dir:
org = 'mouse'
if 'pig' in dir:
org = 'pig'
if 'dog' in dir:
org = 'dog'
if 'rat' in dir:
org = 'rat'
if 'zebrafish' in dir:
org = 'zebrafish'
if metaDict[baseFName][1] == organism:
organismFileList.append(baseFName)
#put small hits for each prediction in dictionary
pCount = {}
smallFile = open(smallFileName, 'r')
currID = 'NONE'
for line in smallFile:
if '\t' not in line: #This is the line with the id in it --> store another ID
currID = line.strip()
else: #this line contains library and count info --> add
lib = line.strip().split('\t')[0]
count = int(line.strip().split('\t')[1])
if cg.getBaseFileName(lib, naked = True) in organismFileList:
if currID in pCount:
pCount[currID] = pCount[currID] + count
else:
pCount[currID] = count
#update the file --> any line with kmer on it give it the count
newLines = []
predFile = open(pFileName, 'r')
for line in predFile:
kmer = line.strip().split('\t')[0].split('.')[0]
if kmer in pCount:
numSmall = pCount[kmer]
else:
numSmall = 0
newLine = line.strip().split('\t')