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)
#how much density for tissue?
import cgConfig
import bioLibCG as cg
mainConf = cgConfig.cgConfig('Main.conf')
conf = cgConfig.cgConfig()
predFile = open(conf.conf['resultsSorted'], 'r') #must be sorted!!!
mirIDs = [x.strip().split('\t')[0].split('.')[0] for x in predFile]
#make lib:tissue dict
metaDict = cg.getMetaFileDict(mainConf.conf['metaFileName'])
#lib is getBaseFileName(key, naked = True): tisue is metaDict[key][3]
#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:
import bioLibCG as cg
import cgConfig
#init
conf = cgConfig.cgConfig()
mainConf = cgConfig.cgConfig('Main.conf')
pFileName = conf.conf['results']
smallFileName = conf.conf['smallAnalysis']
organism = conf.conf['organism']
#make list of acceptable files for organism
organismFileList = [] #NOTE: THESE ARE THE NAKED BASE FILE NAMES!
metaDict = cg.getMetaFileDict(mainConf.conf['metaFileName'])
for baseFName in metaDict:
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:
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)
