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 clipAdapterInDirQ(dirName):
'''The Q if for doing it on a cluster using qsub
Every Q function has a corresponding shell script'''
for file in cg.recurseDir(dirName, end = '.fastq'):
#check if it isn't a clipped file:
if 'clipped' in file:
continue
while True:
#submit job if there are less than ten
if clusterCheck.queryNumJobsQ('chrisgre') < 100:
subprocess.Popen(['qsub', '-V', '-cwd', '-o', 'errors', '-e', 'errors', wrapperShell, file])
time.sleep(.2) #give it time to update qstat
break
else:#wait 10 secs...
time.sleep(10)
def clipAdapterInDirQ(dirName):
'''The Q if for doing it on a cluster using qsub
Every Q function has a corresponding shell script'''
for file in cg.recurseDir(dirName, end='.fastq'):
#check if it isn't a clipped file:
if 'clipped' in file:
continue
while True:
#submit job if there are less than ten
if clusterCheck.queryNumJobsQ('chrisgre') < 100:
subprocess.Popen([
'qsub', '-V', '-cwd', '-o', 'errors', '-e', 'errors',
wrapperShell, file
])
time.sleep(.2) #give it time to update qstat
break
else: #wait 10 secs...
time.sleep(10)
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)
