def markDup(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix = configRobot.popParas(cmdset,['cmd', 'mem', 'time', 'sample', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
programpath = cmdGenerator.checkPath(cmdset.pop('programpath'))
bam = configRobot.popParas(cmdset, 'bam')
jobmanager = jobFactory.jobManager(mem=mem, time=time, overwrite=cmdset.pop('overwrite'))
javacmd = 'java -Xmx%dg -jar'%(int(mem.replace('G',''))-1)
mdupjar = 'MarkDuplicates.jar'
idxcmd = 'samtools index'
for sample in samples:
jobname = prefix + '_' + sample
paraset = copy.deepcopy(cmdset)
paraset['INPUT'] = '=%s/%s'%(inputpath + sample, bam)
paraset['OUTPUT'] = paraset['INPUT'].replace('.bam', '.mdup.bam')
paraset['METRICS_FILE'] = '=%s/%s'%(inputpath + sample, prefix + '_mdupmetrics.txt')
paraset = configRobot.validParas(paraset, availParas[mdupjar])
CMDs = []
CMDs.append( cmdGenerator.formatCmd('source ~/libraries/setup_seqtools') )
CMDs.append( cmdGenerator.formatCmd(javacmd, programpath+mdupjar, paraset) )
CMDs.append( cmdGenerator.formatCmd(idxcmd, paraset['OUTPUT'].strip('=')) )
CMDs.append( cmdGenerator.formatCmd('mv ./%s%s %s'%(jobname, jobmanager.ext, inputpath+sample)) )
jobmanager.createJob(jobname, CMDs, outpath = inputpath+sample, outfn = jobname)
return jobmanager
def cuffcompare(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix, gtf = configRobot.popParas(cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix', 'gtf'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'), create=createpath)
if type(samples) != type([]) and type(samples) != type(()):
samples = [samples]
sampletext = ''
for sample in samples:
sampletext = sampletext + '%s%s/%s '%(inputpath, sample, gtf)
jobmanager = jobFactory.jobManager(mem=mem, time=time, overwrite=cmdset.pop('overwrite'))
jobname = prefix
CMD = []
CMD.append( cmdGenerator.formatCmd('source ~/libraries/setup_seqtools') )
paraset = copy.deepcopy(cmdset)
paraset['-o'] = outputpath + paraset['-o']
paraset = configRobot.validParas(paraset, availParas['cuffcompare'])
CMD.append( cmdGenerator.formatCmd(cmd, paraset, sampletext) )
CMD.append( cmdGenerator.formatCmd('mv ./%s%s %s'%(jobname, jobmanager.ext, outputpath)) )
jobmanager.createJob(jobname, CMD, outpath=outputpath, outfn=jobname, trackcmd=False)
return jobmanager
def RSeQC(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time = configRobot.popParas(cmdset, ['cmd', 'mem', 'time'])
samples, bam, prefix = configRobot.popParas(cmdset, ['sample', 'bam', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'), create=createpath)
programpath = cmdGenerator.checkPath(cmdset.pop('programpath'))
jobmanager = jobFactory.jobManager(mem=mem, time=time, overwrite=cmdset.pop('overwrite'))
programs = ['inner_distance.py', 'junction_annotation.py', 'junction_saturation.py', 'read_GC.py', 'read_duplication.py']
for sample in samples:
jobname = prefix + '_' + sample
CMDs = []
CMDs.append( cmdGenerator.formatCmd('source ~/libraries/setup_seqtools') )
for prog in programs:
paraset = copy.deepcopy(cmdset)
paraset['-i'] = inputpath + sample + '/' + bam
paraset['-o'] = outputpath + sample + '.%s'%(prog.replace('.py', ''))
paraset = configRobot.validParas(paraset, availParas[prog])
if '-o' not in paraset.keys():
paraset['>'] = outputpath + sample + '.%s'%(prog.replace('.py', ''))
CMDs.append( cmdGenerator.formatCmd('python', programpath+prog, paraset) )
CMDs.append( cmdGenerator.formatCmd('mv ./%s%s %s'%(jobname, jobmanager.ext, outputpath)) )
jobmanager.createJob(jobname, CMDs, outpath = outputpath, outfn = jobname)
return jobmanager
def cuffmerge(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix, gtf = configRobot.popParas(
cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix', 'gtf'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'),
create=createpath)
if type(samples) != type([]) and type(samples) != type(()):
samples = [samples]
sampletext = '"'
for sample in samples:
sampletext = sampletext + '%s%s/%s\\n' % (inputpath, sample, gtf)
sampletext = sampletext + '"'
jobmanager = jobFactory.jobManager(mem=mem,
time=time,
overwrite=cmdset.pop('overwrite'))
jobname = prefix
CMD = []
CMD.append(cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
paraset = copy.deepcopy(cmdset)
paraset['-o'] = outputpath + paraset['-o']
CMD.append(
cmdGenerator.formatCmd('echo', sampletext, '>',
paraset['-o'] + '.samples'))
paraset = configRobot.validParas(paraset, availParas['cuffmerge'])
cmdGenerator.checkPath(paraset['-o'], create=createpath)
CMD.append(cmdGenerator.formatCmd(cmd, paraset,
paraset['-o'] + '.samples'))
CMD.append(
cmdGenerator.formatCmd('mv ./%s%s %s' %
(jobname, jobmanager.ext, paraset['-o'])))
CMD.append(cmdGenerator.formatCmd('rm -f', paraset['-o'] + '.samples'))
sgeopt = []
if '-p' in paraset.keys():
if int(paraset['-p']) > 1: #multi threads
sgeopt = ['-pe smp ' + paraset['-p']]
elif '--num-threads' in paraset.keys():
if int(paraset['--num-threads']) > 1:
sgeopt = ['-pe smp ' + paraset['-p']]
jobmanager.createJob(jobname,
CMD,
outpath=paraset['-o'],
outfn=jobname,
sgeopt=sgeopt,
trackcmd=False)
return jobmanager
def cuffdiff_v1(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix, gtf, bam = configRobot.popParas(
cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix', 'gtf', 'bam'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
if type(samples) != type([]) and type(samples) != type(()):
samples = [samples]
sampletext = ''
for sample in samples:
sampletext = sampletext + '%s%s/%s ' % (inputpath, sample, bam)
jobmanager = jobFactory.jobManager(mem=mem,
time=time,
overwrite=cmdset.pop('overwrite'))
jobname = prefix
CMD = []
CMD.append(cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
paraset = copy.deepcopy(cmdset)
paraset = configRobot.validParas(paraset, availParas['cuffdiff'])
cmdGenerator.checkPath(paraset['--output-dir'], create=createpath)
CMD.append(
cmdGenerator.formatCmd(
'/ifs/home/c2b2/dp_lab/bc2252/SeqTool/cufflinks_1/cuffdiff',
paraset, gtf, sampletext))
CMD.append(
cmdGenerator.formatCmd(
'mv ./%s%s %s' %
(jobname, jobmanager.ext, paraset['--output-dir'])))
sgeopt = []
if '-p' in paraset.keys():
if int(paraset['-p']) > 1: #multi threads
sgeopt = ['-pe smp ' + paraset['-p']]
elif '--num-threads' in paraset.keys():
if int(paraset['--num-threads']) > 1:
sgeopt = ['-pe smp ' + paraset['-p']]
jobmanager.createJob(jobname,
CMD,
outpath=paraset['--output-dir'],
outfn=jobname,
sgeopt=sgeopt,
trackcmd=False)
return jobmanager
def picardReorderSam(cmdset, runmode='test'):
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix = configRobot.popParas(
cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'))
programpath = cmdGenerator.checkPath(cmdset.pop('programpath'))
bam = configRobot.popParas(cmdset, 'bam')
jobmanager = jobFactory.jobManager(mem=mem,
time=time,
overwrite=cmdset.pop('overwrite'))
if '-Djava.io.tmpdir' in cmdset.keys():
javacmd = 'java ' + '-Djava.io.tmpdir' + cmdGenerator.checkPath(
cmdset.pop('-Djava.io.tmpdir'))
else:
javacmd = 'java'
javacmd = javacmd + ' -Xmx%dg -jar' % (int(mem.replace('G', '')) - 2)
reorder = programpath + 'ReorderSam.jar VALIDATION_STRINGENCY=LENIENT'
for sample in samples:
CMDs = []
CMDs.append(
cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
jobname = prefix + '_' + sample
#reorder by chrm
paraset = copy.deepcopy(cmdset)
if bam == '=sample':
inputfile = sample
else:
inputfile = sample + '/' + bam
paraset['INPUT'] = '=%s' % (inputpath + inputfile)
paraset['OUTPUT'] = '=%s.reorder.bam' % (outputpath +
inputfile.replace('.bam', ''))
paraset = configRobot.validParas(paraset, availParas['ReorderSam.jar'])
CMDs.append(cmdGenerator.formatCmd(javacmd, reorder, paraset))
CMDs.append(
cmdGenerator.formatCmd('mv ./%s%s %s' %
(jobname, jobmanager.ext, outputpath)))
jobmanager.createJob(jobname, CMDs, outpath=outputpath, outfn=jobname)
return jobmanager
def cufflinks(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix, bam = configRobot.popParas(
cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix', 'bam'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'),
create=createpath)
outputpath = cmdGenerator.checkPath(outputpath + '%s/' % prefix,
create=createpath)
if type(samples) != type([]) and type(samples) != type(()):
samples = [samples]
jobmanager = jobFactory.jobManager(mem=mem,
time=time,
overwrite=cmdset.pop('overwrite'))
for sample in samples:
jobname = prefix + '_' + sample
CMD = []
CMD.append(cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
paraset = copy.deepcopy(cmdset)
paraset['-o'] = outputpath + sample
paraset = configRobot.validParas(paraset, availParas['cufflinks'])
cmdGenerator.checkPath(paraset['-o'], create=createpath)
CMD.append(
cmdGenerator.formatCmd(cmd, paraset,
inputpath + '%s/' % sample + bam))
CMD.append(
cmdGenerator.formatCmd('mv ./%s%s %s' %
(jobname, jobmanager.ext, paraset['-o'])))
sgeopt = []
if '-p' in paraset.keys():
if int(paraset['-p']) > 1: #multi threads
sgeopt = ['-pe smp ' + paraset['-p']]
elif '--num-threads' in paraset.keys():
if int(paraset['--num-threads']) > 1:
sgeopt = ['-pe smp ' + paraset['-p']]
jobmanager.createJob(jobname,
CMD,
outpath=paraset['-o'],
outfn=jobname,
sgeopt=sgeopt)
return jobmanager
def picardQC(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, bam, prefix = configRobot.popParas(cmdset, ['cmd', 'mem', 'time', 'bam', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'), create=createpath)
programpath = cmdGenerator.checkPath(cmdset.pop('programpath'))
samples = cmdset.pop('sample')
javacmd = 'java -Xmx%dg -jar'%(int(mem.replace('G',''))-2)
jobmanager = jobFactory.jobManager(mem=mem, time=time, overwrite=cmdset.pop('overwrite'))
metrics = {'CollectRnaSeqMetrics.jar': 'RnaSeq', 'CollectMultipleMetrics.jar': '', 'EstimateLibraryComplexity.jar': 'Lib', 'CollectGcBiasMetrics.jar': 'GC'}
metrickeys = ['CollectRnaSeqMetrics.jar', 'CollectMultipleMetrics.jar', 'EstimateLibraryComplexity.jar', 'CollectGcBiasMetrics.jar']
for sample in samples:
jobname = prefix + '_' + sample
allcmds = []
allcmds.append(cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
paraset = copy.deepcopy(cmdset)
if bam == '=sample':
paraset['INPUT'] = '=%s'%(inputpath+sample)
else:
paraset['INPUT'] = '=%s/%s'%(inputpath+sample, bam)
paraset['TMP_DIR'] = paraset['TMP_DIR'] + prefix + '_' + sample + '/'
cmdGenerator.checkPath(paraset['TMP_DIR'].strip('='), create=createpath)
for metric in metrickeys:
if 'MultipleMetrics' in metric:
paraset['OUTPUT'] = '=%s'%(outputpath + sample + metrics[metric])
else:
paraset['OUTPUT'] = '=%s.txt'%(outputpath + sample + '.' + metrics[metric])
paraset['CHART_OUTPUT'] = '%s'%(paraset['OUTPUT'].replace('.txt', '.pdf'))
paraset['SUMMARY_OUTPUT'] = '%s'%(paraset['OUTPUT'].replace('.txt', '.summary.txt'))
#filter out parameters that are not supported
metricparaset = configRobot.validParas(paraset, availParas[metric])
allcmds.append(cmdGenerator.formatCmd(javacmd, programpath + metric, metricparaset))
allcmds.append(cmdGenerator.formatCmd('mv ./%s%s %s'%(jobname, jobmanager.ext, outputpath)))
allcmds.append(cmdGenerator.formatCmd('rm -Rf', paraset['TMP_DIR'].strip('=')))
jobmanager.createJob(jobname, allcmds, outpath = outputpath, outfn = jobname)
return jobmanager
def RSeQC(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time = configRobot.popParas(cmdset, ['cmd', 'mem', 'time'])
samples, bam, prefix = configRobot.popParas(cmdset,
['sample', 'bam', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'),
create=createpath)
programpath = cmdGenerator.checkPath(cmdset.pop('programpath'))
jobmanager = jobFactory.jobManager(mem=mem,
time=time,
overwrite=cmdset.pop('overwrite'))
programs = [
'inner_distance.py', 'junction_annotation.py',
'junction_saturation.py', 'read_GC.py', 'read_duplication.py'
]
for sample in samples:
jobname = prefix + '_' + sample
CMDs = []
CMDs.append(
cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
for prog in programs:
paraset = copy.deepcopy(cmdset)
paraset['-i'] = inputpath + sample + '/' + bam
paraset['-o'] = outputpath + sample + '.%s' % (prog.replace(
'.py', ''))
paraset = configRobot.validParas(paraset, availParas[prog])
if '-o' not in paraset.keys():
paraset['>'] = outputpath + sample + '.%s' % (prog.replace(
'.py', ''))
CMDs.append(
cmdGenerator.formatCmd('python', programpath + prog, paraset))
CMDs.append(
cmdGenerator.formatCmd('mv ./%s%s %s' %
(jobname, jobmanager.ext, outputpath)))
jobmanager.createJob(jobname, CMDs, outpath=outputpath, outfn=jobname)
return jobmanager
def markDup(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix = configRobot.popParas(
cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
programpath = cmdGenerator.checkPath(cmdset.pop('programpath'))
bam = configRobot.popParas(cmdset, 'bam')
jobmanager = jobFactory.jobManager(mem=mem,
time=time,
overwrite=cmdset.pop('overwrite'))
javacmd = 'java -Xmx%dg -jar' % (int(mem.replace('G', '')) - 1)
mdupjar = 'MarkDuplicates.jar'
idxcmd = 'samtools index'
for sample in samples:
jobname = prefix + '_' + sample
paraset = copy.deepcopy(cmdset)
paraset['INPUT'] = '=%s/%s' % (inputpath + sample, bam)
paraset['OUTPUT'] = paraset['INPUT'].replace('.bam', '.mdup.bam')
paraset['METRICS_FILE'] = '=%s/%s' % (inputpath + sample,
prefix + '_mdupmetrics.txt')
paraset = configRobot.validParas(paraset, availParas[mdupjar])
CMDs = []
CMDs.append(
cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
CMDs.append(
cmdGenerator.formatCmd(javacmd, programpath + mdupjar, paraset))
CMDs.append(
cmdGenerator.formatCmd(idxcmd, paraset['OUTPUT'].strip('=')))
CMDs.append(
cmdGenerator.formatCmd(
'mv ./%s%s %s' %
(jobname, jobmanager.ext, inputpath + sample)))
jobmanager.createJob(jobname,
CMDs,
outpath=inputpath + sample,
outfn=jobname)
return jobmanager
def picardReorderSam(cmdset, runmode='test'):
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix = configRobot.popParas(cmdset,['cmd', 'mem', 'time', 'sample', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'))
programpath = cmdGenerator.checkPath(cmdset.pop('programpath'))
bam = configRobot.popParas(cmdset, 'bam')
jobmanager = jobFactory.jobManager(mem=mem, time=time, overwrite=cmdset.pop('overwrite'))
if '-Djava.io.tmpdir' in cmdset.keys():
javacmd = 'java ' + '-Djava.io.tmpdir' + cmdGenerator.checkPath(cmdset.pop('-Djava.io.tmpdir'))
else:
javacmd = 'java'
javacmd = javacmd + ' -Xmx%dg -jar'%(int(mem.replace('G',''))-2)
reorder = programpath + 'ReorderSam.jar VALIDATION_STRINGENCY=LENIENT'
for sample in samples:
CMDs = []
CMDs.append( cmdGenerator.formatCmd('source ~/libraries/setup_seqtools') )
jobname = prefix + '_' + sample
#reorder by chrm
paraset = copy.deepcopy(cmdset)
if bam == '=sample':
inputfile = sample
else:
inputfile = sample + '/' + bam
paraset['INPUT'] = '=%s'%(inputpath + inputfile)
paraset['OUTPUT'] = '=%s.reorder.bam'%(outputpath + inputfile.replace('.bam',''))
paraset = configRobot.validParas(paraset, availParas['ReorderSam.jar'])
CMDs.append( cmdGenerator.formatCmd(javacmd, reorder, paraset) )
CMDs.append( cmdGenerator.formatCmd('mv ./%s%s %s'%(jobname, jobmanager.ext, outputpath)) )
jobmanager.createJob(jobname, CMDs, outpath = outputpath, outfn = jobname)
return jobmanager
def cuffmerge(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix, gtf = configRobot.popParas(cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix', 'gtf'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'), create=createpath)
if type(samples) != type([]) and type(samples) != type(()):
samples = [samples]
sampletext = '"'
for sample in samples:
sampletext = sampletext + '%s%s/%s\\n'%(inputpath, sample, gtf)
sampletext = sampletext + '"'
jobmanager = jobFactory.jobManager(mem=mem, time=time, overwrite=cmdset.pop('overwrite'))
jobname = prefix
CMD = []
CMD.append( cmdGenerator.formatCmd('source ~/libraries/setup_seqtools') )
paraset = copy.deepcopy(cmdset)
paraset['-o'] = outputpath + paraset['-o']
CMD.append( cmdGenerator.formatCmd('echo', sampletext, '>', paraset['-o'] + '.samples') )
paraset = configRobot.validParas(paraset, availParas['cuffmerge'])
cmdGenerator.checkPath(paraset['-o'], create=createpath)
CMD.append( cmdGenerator.formatCmd(cmd, paraset, paraset['-o'] + '.samples') )
CMD.append( cmdGenerator.formatCmd('mv ./%s%s %s'%(jobname, jobmanager.ext, paraset['-o'])) )
CMD.append( cmdGenerator.formatCmd('rm -f', paraset['-o'] + '.samples') )
sgeopt = []
if '-p' in paraset.keys():
if int(paraset['-p']) > 1: #multi threads
sgeopt = ['-pe smp ' + paraset['-p']]
elif '--num-threads' in paraset.keys():
if int(paraset['--num-threads']) > 1:
sgeopt = ['-pe smp ' + paraset['-p']]
jobmanager.createJob(jobname, CMD, outpath=paraset['-o'], outfn=jobname, sgeopt=sgeopt, trackcmd=False)
return jobmanager
def cuffcompare(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix, gtf = configRobot.popParas(
cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix', 'gtf'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'),
create=createpath)
if type(samples) != type([]) and type(samples) != type(()):
samples = [samples]
sampletext = ''
for sample in samples:
sampletext = sampletext + '%s%s/%s ' % (inputpath, sample, gtf)
jobmanager = jobFactory.jobManager(mem=mem,
time=time,
overwrite=cmdset.pop('overwrite'))
jobname = prefix
CMD = []
CMD.append(cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
paraset = copy.deepcopy(cmdset)
paraset['-o'] = outputpath + paraset['-o']
paraset = configRobot.validParas(paraset, availParas['cuffcompare'])
CMD.append(cmdGenerator.formatCmd(cmd, paraset, sampletext))
CMD.append(
cmdGenerator.formatCmd('mv ./%s%s %s' %
(jobname, jobmanager.ext, outputpath)))
jobmanager.createJob(jobname,
CMD,
outpath=outputpath,
outfn=jobname,
trackcmd=False)
return jobmanager
def cufflinks(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix, bam = configRobot.popParas(cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix', 'bam'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'), create=createpath)
outputpath = cmdGenerator.checkPath(outputpath + '%s/'%prefix, create=createpath)
if type(samples) != type([]) and type(samples) != type(()):
samples = [samples]
jobmanager = jobFactory.jobManager(mem=mem, time=time, overwrite=cmdset.pop('overwrite'))
for sample in samples:
jobname = prefix + '_' + sample
CMD = []
CMD.append( cmdGenerator.formatCmd('source ~/libraries/setup_seqtools') )
paraset = copy.deepcopy(cmdset)
paraset['-o'] = outputpath + sample
paraset = configRobot.validParas(paraset, availParas['cufflinks'])
cmdGenerator.checkPath(paraset['-o'], create=createpath)
CMD.append( cmdGenerator.formatCmd(cmd, paraset, inputpath+'%s/'%sample+bam) )
CMD.append( cmdGenerator.formatCmd('mv ./%s%s %s'%(jobname, jobmanager.ext, paraset['-o'])) )
sgeopt = []
if '-p' in paraset.keys():
if int(paraset['-p']) > 1: #multi threads
sgeopt = ['-pe smp ' + paraset['-p']]
elif '--num-threads' in paraset.keys():
if int(paraset['--num-threads']) > 1:
sgeopt = ['-pe smp ' + paraset['-p']]
jobmanager.createJob(jobname, CMD, outpath=paraset['-o'], outfn=jobname, sgeopt=sgeopt)
return jobmanager
def cuffdiff_v1(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix, gtf, bam = configRobot.popParas(cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix', 'gtf', 'bam'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
if type(samples) != type([]) and type(samples) != type(()):
samples = [samples]
sampletext = ''
for sample in samples:
sampletext = sampletext + '%s%s/%s '%(inputpath, sample, bam)
jobmanager = jobFactory.jobManager(mem=mem, time=time, overwrite=cmdset.pop('overwrite'))
jobname = prefix
CMD = []
CMD.append( cmdGenerator.formatCmd('source ~/libraries/setup_seqtools') )
paraset = copy.deepcopy(cmdset)
paraset = configRobot.validParas(paraset, availParas['cuffdiff'])
cmdGenerator.checkPath(paraset['--output-dir'], create=createpath)
CMD.append( cmdGenerator.formatCmd('/ifs/home/c2b2/dp_lab/bc2252/SeqTool/cufflinks_1/cuffdiff', paraset, gtf, sampletext) )
CMD.append( cmdGenerator.formatCmd('mv ./%s%s %s'%(jobname, jobmanager.ext, paraset['--output-dir'])) )
sgeopt = []
if '-p' in paraset.keys():
if int(paraset['-p']) > 1: #multi threads
sgeopt = ['-pe smp ' + paraset['-p']]
elif '--num-threads' in paraset.keys():
if int(paraset['--num-threads']) > 1:
sgeopt = ['-pe smp ' + paraset['-p']]
jobmanager.createJob(jobname, CMD, outpath=paraset['--output-dir'], outfn=jobname, sgeopt=sgeopt, trackcmd=False)
return jobmanager
def picardQC(cmdset, runmode='test'):
global availParas
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, bam, prefix = configRobot.popParas(
cmdset, ['cmd', 'mem', 'time', 'bam', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
outputpath = cmdGenerator.checkPath(cmdset.pop('outputpath'),
create=createpath)
programpath = cmdGenerator.checkPath(cmdset.pop('programpath'))
samples = cmdset.pop('sample')
javacmd = 'java -Xmx%dg -jar' % (int(mem.replace('G', '')) - 2)
jobmanager = jobFactory.jobManager(mem=mem,
time=time,
overwrite=cmdset.pop('overwrite'))
metrics = {
'CollectRnaSeqMetrics.jar': 'RnaSeq',
'CollectMultipleMetrics.jar': '',
'EstimateLibraryComplexity.jar': 'Lib',
'CollectGcBiasMetrics.jar': 'GC'
}
metrickeys = [
'CollectRnaSeqMetrics.jar', 'CollectMultipleMetrics.jar',
'EstimateLibraryComplexity.jar', 'CollectGcBiasMetrics.jar'
]
for sample in samples:
jobname = prefix + '_' + sample
allcmds = []
allcmds.append(
cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
paraset = copy.deepcopy(cmdset)
if bam == '=sample':
paraset['INPUT'] = '=%s' % (inputpath + sample)
else:
paraset['INPUT'] = '=%s/%s' % (inputpath + sample, bam)
paraset['TMP_DIR'] = paraset['TMP_DIR'] + prefix + '_' + sample + '/'
cmdGenerator.checkPath(paraset['TMP_DIR'].strip('='),
create=createpath)
for metric in metrickeys:
if 'MultipleMetrics' in metric:
paraset['OUTPUT'] = '=%s' % (outputpath + sample +
metrics[metric])
else:
paraset['OUTPUT'] = '=%s.txt' % (outputpath + sample + '.' +
metrics[metric])
paraset['CHART_OUTPUT'] = '%s' % (paraset['OUTPUT'].replace(
'.txt', '.pdf'))
paraset['SUMMARY_OUTPUT'] = '%s' % (paraset['OUTPUT'].replace(
'.txt', '.summary.txt'))
#filter out parameters that are not supported
metricparaset = configRobot.validParas(paraset, availParas[metric])
allcmds.append(
cmdGenerator.formatCmd(javacmd, programpath + metric,
metricparaset))
allcmds.append(
cmdGenerator.formatCmd('mv ./%s%s %s' %
(jobname, jobmanager.ext, outputpath)))
allcmds.append(
cmdGenerator.formatCmd('rm -Rf', paraset['TMP_DIR'].strip('=')))
jobmanager.createJob(jobname,
allcmds,
outpath=outputpath,
outfn=jobname)
return jobmanager
def preGATK(cmdset, runmode='test'):
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix = configRobot.popParas(
cmdset, ['cmd', 'mem', 'time', 'sample', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
picardpath = cmdGenerator.checkPath(cmdset.pop('picardpath'))
gatkpath = cmdGenerator.checkPath(cmdset.pop('gatkpath'))
bam = configRobot.popParas(cmdset, 'bam')
jobmanager = jobFactory.jobManager(mem=mem,
time=time,
overwrite=cmdset.pop('overwrite'))
if '-Djava.io.tmpdir' in cmdset.keys():
javacmd = 'java ' + '-Djava.io.tmpdir' + cmdGenerator.checkPath(
cmdset.pop('-Djava.io.tmpdir'))
else:
javacmd = 'java'
javacmd = javacmd + ' -Xmx%dg -jar' % (int(mem.replace('G', '')) - 2)
samview = 'samtools view -b -h -F 264'
reorder = picardpath + 'ReorderSam.jar VALIDATION_STRINGENCY=LENIENT'
RG = picardpath + 'AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT RGLB=dUTP RGPL=illumina RGPU=1'
mdupjar = picardpath + 'MarkDuplicates.jar'
GATK = gatkpath + 'GenomeAnalysisTK.jar '
createTg = '-T RealignerTargetCreator '
realign = '-T IndelRealigner '
idxcmd = 'samtools index'
clearup = 'rm -f '
for sample in samples:
CMDs = []
CMDs.append(
cmdGenerator.formatCmd('source ~/libraries/setup_seqtools'))
jobname = prefix + '_' + sample
#filter
paraset = copy.deepcopy(cmdset)
paraset['-o'] = '%s/%s.filter.bam' % (inputpath + sample,
bam.replace('.bam', ''))
lastoutput = paraset['-o']
del paraset['-R']
del paraset['-filterMBQ']
#paraset = configRobot.validParas(paraset, availParas['samtools'])
CMDs.append(
cmdGenerator.formatCmd(samview, paraset,
inputpath + sample + '/' + bam))
#reorder by chrm
paraset = copy.deepcopy(cmdset)
paraset['INPUT'] = '=%s' % lastoutput
paraset['OUTPUT'] = '=%s.reorder.bam' % (lastoutput.replace(
'.bam', ''))
paraset['REFERENCE'] = '=%s' % paraset['-R']
paraset = configRobot.validParas(paraset, availParas['ReorderSam.jar'])
CMDs.append(cmdGenerator.formatCmd(javacmd, reorder, paraset))
CMDs.append(cmdGenerator.formatCmd(clearup, lastoutput))
lastoutput = paraset['OUTPUT'].strip('=')
#add RG
paraset = copy.deepcopy(cmdset)
paraset['INPUT'] = '=%s' % lastoutput
paraset['OUTPUT'] = '=%s.addRG.bam' % (lastoutput.replace('.bam', ''))
paraset['RGSM'] = '=%s' % sample
paraset = configRobot.validParas(
paraset, availParas['AddOrReplaceReadGroups.jar'])
CMDs.append(cmdGenerator.formatCmd(javacmd, RG, paraset))
CMDs.append(cmdGenerator.formatCmd(clearup, lastoutput))
lastoutput = paraset['OUTPUT'].strip('=')
#mark duplicates
paraset = copy.deepcopy(cmdset)
paraset['INPUT'] = '=%s' % lastoutput
paraset['OUTPUT'] = '=%s.mdup.bam' % (lastoutput.replace('.bam', ''))
paraset['METRICS_FILE'] = '=%s/%s' % (inputpath + sample,
prefix + '_mdupmetrics.txt')
paraset = configRobot.validParas(paraset,
availParas['MarkDuplicates.jar'])
CMDs.append(cmdGenerator.formatCmd(javacmd, mdupjar, paraset))
CMDs.append(
cmdGenerator.formatCmd(idxcmd, paraset['OUTPUT'].strip('=')))
lastoutput = paraset['OUTPUT'].strip('=')
#create intervals
paraset = copy.deepcopy(cmdset)
paraset['-I'] = lastoutput
paraset['-o'] = lastoutput.replace('.bam', '.intervals')
CMDs.append(cmdGenerator.formatCmd(javacmd, GATK + createTg, paraset))
#realign
paraset['-targetIntervals'] = paraset['-o']
paraset['-o'] = lastoutput.replace('.bam', '.realign.bam')
CMDs.append(cmdGenerator.formatCmd(javacmd, GATK + realign, paraset))
#clear up
CMDs.append(cmdGenerator.formatCmd(clearup, lastoutput))
CMDs.append(
cmdGenerator.formatCmd(clearup,
lastoutput.replace('.bam', '.intervals')))
CMDs.append(
cmdGenerator.formatCmd(
'mv ./%s%s %s' %
(jobname, jobmanager.ext, inputpath + sample)))
jobmanager.createJob(jobname,
CMDs,
outpath=inputpath + sample,
outfn=jobname)
return jobmanager
def preGATK(cmdset, runmode='test'):
if runmode == 'test':
createpath = False
else:
createpath = True
cmd, mem, time, samples, prefix = configRobot.popParas(cmdset,['cmd', 'mem', 'time', 'sample', 'prefix'])
inputpath = cmdGenerator.checkPath(cmdset.pop('inputpath'))
picardpath = cmdGenerator.checkPath(cmdset.pop('picardpath'))
gatkpath = cmdGenerator.checkPath(cmdset.pop('gatkpath'))
bam = configRobot.popParas(cmdset, 'bam')
jobmanager = jobFactory.jobManager(mem=mem, time=time, overwrite=cmdset.pop('overwrite'))
if '-Djava.io.tmpdir' in cmdset.keys():
javacmd = 'java ' + '-Djava.io.tmpdir' + cmdGenerator.checkPath(cmdset.pop('-Djava.io.tmpdir'))
else:
javacmd = 'java'
javacmd = javacmd + ' -Xmx%dg -jar'%(int(mem.replace('G',''))-2)
samview = 'samtools view -b -h -F 264'
reorder = picardpath + 'ReorderSam.jar VALIDATION_STRINGENCY=LENIENT'
RG = picardpath + 'AddOrReplaceReadGroups.jar VALIDATION_STRINGENCY=LENIENT RGLB=dUTP RGPL=illumina RGPU=1'
mdupjar = picardpath + 'MarkDuplicates.jar'
GATK = gatkpath + 'GenomeAnalysisTK.jar '
createTg = '-T RealignerTargetCreator '
realign = '-T IndelRealigner '
idxcmd = 'samtools index'
clearup = 'rm -f '
for sample in samples:
CMDs = []
CMDs.append( cmdGenerator.formatCmd('source ~/libraries/setup_seqtools') )
jobname = prefix + '_' + sample
#filter
paraset = copy.deepcopy(cmdset)
paraset['-o'] = '%s/%s.filter.bam'%(inputpath+sample, bam.replace('.bam',''))
lastoutput = paraset['-o']
del paraset['-R']
del paraset['-filterMBQ']
#paraset = configRobot.validParas(paraset, availParas['samtools'])
CMDs.append( cmdGenerator.formatCmd(samview, paraset, inputpath+sample+'/'+bam ) )
#reorder by chrm
paraset = copy.deepcopy(cmdset)
paraset['INPUT'] = '=%s'%lastoutput
paraset['OUTPUT'] = '=%s.reorder.bam'%(lastoutput.replace('.bam',''))
paraset['REFERENCE'] = '=%s'%paraset['-R']
paraset = configRobot.validParas(paraset, availParas['ReorderSam.jar'])
CMDs.append( cmdGenerator.formatCmd(javacmd, reorder, paraset) )
CMDs.append( cmdGenerator.formatCmd(clearup, lastoutput) )
lastoutput = paraset['OUTPUT'].strip('=')
#add RG
paraset = copy.deepcopy(cmdset)
paraset['INPUT'] = '=%s'%lastoutput
paraset['OUTPUT'] = '=%s.addRG.bam'%(lastoutput.replace('.bam',''))
paraset['RGSM'] = '=%s'%sample
paraset = configRobot.validParas(paraset, availParas['AddOrReplaceReadGroups.jar'])
CMDs.append( cmdGenerator.formatCmd(javacmd, RG, paraset) )
CMDs.append( cmdGenerator.formatCmd(clearup, lastoutput) )
lastoutput = paraset['OUTPUT'].strip('=')
#mark duplicates
paraset = copy.deepcopy(cmdset)
paraset['INPUT'] = '=%s'%lastoutput
paraset['OUTPUT'] = '=%s.mdup.bam'%(lastoutput.replace('.bam', ''))
paraset['METRICS_FILE'] = '=%s/%s'%(inputpath + sample, prefix + '_mdupmetrics.txt')
paraset = configRobot.validParas(paraset, availParas['MarkDuplicates.jar'])
CMDs.append( cmdGenerator.formatCmd(javacmd, mdupjar, paraset) )
CMDs.append( cmdGenerator.formatCmd(idxcmd, paraset['OUTPUT'].strip('=')) )
lastoutput = paraset['OUTPUT'].strip('=')
#create intervals
paraset = copy.deepcopy(cmdset)
paraset['-I'] = lastoutput
paraset['-o'] = lastoutput.replace('.bam', '.intervals')
CMDs.append( cmdGenerator.formatCmd(javacmd, GATK+createTg, paraset) )
#realign
paraset['-targetIntervals'] = paraset['-o']
paraset['-o'] = lastoutput.replace('.bam', '.realign.bam')
CMDs.append( cmdGenerator.formatCmd(javacmd, GATK+realign, paraset) )
#clear up
CMDs.append( cmdGenerator.formatCmd(clearup, lastoutput) )
CMDs.append( cmdGenerator.formatCmd(clearup, lastoutput.replace('.bam', '.intervals')) )
CMDs.append( cmdGenerator.formatCmd('mv ./%s%s %s'%(jobname, jobmanager.ext, inputpath+sample)) )
jobmanager.createJob(jobname, CMDs, outpath = inputpath+sample, outfn = jobname)
return jobmanager
