def merge_results(name, sample):
for r in sample.replicates + [
sample.combined_replicate,
]:
for q_val in sample.conf.Q_VALUE_THRESHOLDS + [
0,
]:
if q_val:
output = os.path.join(
r.results_dir(sample),
'%s_%f_hits_filtered.bed' % (r.rep_name(sample), q_val))
else:
output = os.path.join(
r.results_dir(sample),
'%s_hits_filtered.bed' % r.rep_name(sample))
r.unfiltered_results = output
cmd = filter_hits_cmd(r.results_dir(sample), r.sgr_dir(sample),
sample.genome, output, q_val)
sample.add_jobs(name, [
sjm.Job('merge_' + r.rep_name(sample) + '%g' % (q_val), [
cmd,
],
queue=QUEUE,
project=PROJECT,
sched_options="-m e"),
])
# Merge Pseudoreplicate Hits
output = os.path.join(r.results_dir(sample),
'%s_hits.bed' % (r.rep_name(sample) + '_PR1'))
r.unfiltered_results_pr1 = output
cmd = filter_hits_cmd(r.pr1_results_dir, r.pr1_sgr_dir, sample.genome,
output)
sample.add_jobs(name, [
sjm.Job('merge_' + r.rep_name(sample) + '_PR1', [
cmd,
],
queue=QUEUE,
project=PROJECT,
sched_options="-m e"),
])
output = os.path.join(r.results_dir(sample),
'%s_hits.bed' % (r.rep_name(sample) + '_PR2'))
r.unfiltered_results_pr2 = output
cmd = filter_hits_cmd(r.pr1_results_dir, r.pr1_sgr_dir, sample.genome,
output)
sample.add_jobs(name, [
sjm.Job('merge_' + r.rep_name(sample) + '_PR2', [
cmd,
],
queue=QUEUE,
project=PROJECT,
sched_options="-m e"),
])
def idr_analysis(name, sample):
jobs = []
modules = ["r/3.0.1"]
for i, rep_a in enumerate(sample.replicates):
for j in range(i + 1, len(sample.replicates)):
rep_b = sample.replicates[j]
idr_name = '%s_VS_%s' % (rep_a.rep_name(sample),
rep_b.rep_name(sample))
cmd = idr.idr_analysis_cmd(rep_a.narrowPeak, rep_b.narrowPeak,
os.path.join(sample.idr_dir, idr_name),
'q.value', sample.genome)
jobs.append(
sjm.Job('idr_analysis_' + idr_name, [
cmd,
],
queue=QUEUE,
modules=modules,
project=PROJECT,
sched_options="-m e"))
# Pseudoreplicates
idr_name = '%s_PR1_VS_%s_PR2' % (rep_a.rep_name(sample),
rep_a.rep_name(sample))
cmd = idr.idr_analysis_cmd(
rep_a.narrowPeak_pr1, rep_a.narrowPeak_pr2,
os.path.join(sample.idr_dir, idr_name + '_PR'), 'q.value',
sample.genome)
jobs.append(
sjm.Job('idr_analysis_' + idr_name, [
cmd,
],
queue=QUEUE,
modules=modules,
project=PROJECT,
sched_options="-m e"))
# Pooled Pseudoreplicates
idr_name = '%s_PR1_VS_%s_PR2' % (sample.combined_replicate.rep_name(
sample), sample.combined_replicate.rep_name(sample))
cmd = idr.idr_analysis_cmd(sample.combined_replicate.narrowPeak_pr1,
sample.combined_replicate.narrowPeak_pr2,
os.path.join(sample.idr_dir, idr_name),
'q.value', sample.genome)
jobs.append(
sjm.Job('idr_analysis_' + idr_name, [
cmd,
],
queue=QUEUE,
modules=modules,
project=PROJECT,
sched_options="-m e"))
sample.add_jobs(name, jobs)
def main(gvcfs):
jobs = merge_gvcf(gvcfs)
jobs = gatk_joint(jobs)
descout = sys.stdout if jobfile is None else open(jobfile.path, "w")
descout.write(sjm.Job().depend(*jobs).desc())
descout.flush()
def replicate_scoring(name, sample):
cmds = []
# Mapped Read Statistics
cmd = os.path.join(BIN_DIR, 'read_stats.py')
cmd += ' %s' % os.path.join(sample.results_dir, 'rep_stats')
cmd += ' ' + sample.conf.path
cmds.append(cmd)
# Replicate Overlap Statistics
for q in sample.conf.Q_VALUE_THRESHOLDS:
for r1 in sample.replicates:
for r2 in sample.replicates:
if r1 == r2:
continue
cmd = os.path.join(BIN_DIR, 'overlap_stats.py')
cmd += ' ' + r1.narrowPeak
cmd += ' ' + r2.narrowPeak
cmd += ' ' + os.path.join(sample.results_dir, 'rep_stats')
cmd += ' %f' % q
cmd += ' %s_VS_%s_%f' % (r1.rep_name(sample),
r2.rep_name(sample), q)
cmds.append(cmd)
j = sjm.Job('replicate_stats',
cmds,
queue=QUEUE,
project=PROJECT,
sched_options="-m e")
sample.add_jobs(name, [
j,
])
def mail_results(sample, control, run_name, emails):
cmds = []
cmd = os.path.join(BIN_DIR, 'build_report_text.py')
cmd += ' %s' % sample.run_name
cmd += ' %s' % sample.archive_file_download
cmd += ' %s' % control.archive_file_download
cmd += ' %s' % os.path.join(sample.results_dir, 'rep_stats')
cmd += ' %s' % os.path.join(sample.results_dir, 'spp_stats.txt')
cmd += ' %s' % os.path.join(sample.results_dir, 'idr_results.txt')
cmd += ' %s' % os.path.join(sample.results_dir, 'pbc_stats.txt')
cmd += ' %s' % os.path.join(sample.results_dir, 'full_report.txt')
cmds.append(cmd)
cmd = os.path.join(BIN_DIR, 'mail_wrapper.py')
cmd += ' "%s Scoring Results"' % sample.run_name
cmd += ' %s' % os.path.join(sample.results_dir, 'full_report.txt')
for email in emails:
cmd += ' %s' % email
cmds.append(cmd)
return sjm.Job('mail_results',
cmds,
queue=QUEUE,
project=PROJECT,
host='localhost',
sched_options="-m e",
dependencies=sample.all_jobs() + control.all_jobs())
def form_control_files(name, control):
print " ******* form control files ****** "
cmds = []
control.merged_file_location = os.path.join(
control.temp_dir, '%s_merged_eland.txt' % control.run_name)
print " merged conrol files ", control.merged_file_location
# Merge eland files
cmd = os.path.join(BIN_DIR, 'merge_and_filter_reads.py')
cmd += ' %s' % control.merged_file_location
print " merged conrol files ", cmd
#sys.exit()
for mr in control.mapped_read_files:
cmd += ' %s' % mr
cmds.append(cmd)
# Divide merged file by chr
cmd = os.path.join(BIN_DIR, 'divide_eland.py')
cmd += " %s %s %s" % (control.merged_file_location, control.genome,
control.results_dir)
cmds.append(cmd)
# Create Signal Map
cmd = os.path.join(BIN_DIR, 'create_signal_map.py')
cmd += ' %s %s' % (control.sgr_dir, control.results_dir)
cmds.append(cmd)
control.add_jobs(name, [
sjm.Job(control.run_name,
cmds,
modules=["samtools/1.2"],
queue=QUEUE,
project=PROJECT,
sched_options="-m e"),
])
def form_idr_inputs(name, sample):
os.makedirs(os.path.join(sample.results_dir, 'idr'))
jobs = []
for rep in sample.replicates + [
sample.combined_replicate,
]:
rep.narrowPeak = os.path.join(
rep.results_dir(sample),
rep.rep_name(sample) + '_unfiltered_narrowPeak.bed')
cmd = os.path.join(SUBMISSION_BIN_DIR, 'normalhits2narrowPeak')
cmd += ' %s > %s' % (rep.unfiltered_results, rep.narrowPeak)
jobs.append(
sjm.Job(rep.rep_name(sample) + '_hits2narrowPeak', [
cmd,
],
queue=QUEUE,
project=PROJECT,
sched_options="-m e"))
# Pseudoreplicates
rep.narrowPeak_pr1 = os.path.join(
rep.results_dir(sample),
rep.rep_name(sample) + '_PR1_unfiltered_narrowPeak.bed')
cmd = os.path.join(SUBMISSION_BIN_DIR, 'normalhits2narrowPeak')
cmd += ' %s > %s' % (rep.unfiltered_results_pr1, rep.narrowPeak_pr1)
jobs.append(
sjm.Job(rep.rep_name(sample) + '_PR1_hits2narrowPeak', [
cmd,
],
queue=QUEUE,
project=PROJECT,
sched_options="-m e"))
rep.narrowPeak_pr2 = os.path.join(
rep.results_dir(sample),
rep.rep_name(sample) + '_PR2_unfiltered_narrowPeak.bed')
cmd = os.path.join(SUBMISSION_BIN_DIR, 'normalhits2narrowPeak')
cmd += ' %s > %s' % (rep.unfiltered_results_pr2, rep.narrowPeak_pr2)
jobs.append(
sjm.Job(rep.rep_name(sample) + '_PR2_hits2narrowPeak', [
cmd,
],
queue=QUEUE,
project=PROJECT,
sched_options="-m e"))
sample.add_jobs(name, jobs)
def gatk_vqsr(pjob):
jobs = []
vcf = pjob.output
job = sjm.Job('gatk_VQSR-%s' % (vcf.prefix))
job.memory = "10G"
job.append('gatk_vqsr.sh %s' % vcf)
job.depend(pjob)
return job
def gatk_mvcf(pjobs, vcfout):
vcfs = [pjob.output for pjob in pjobs]
job = sjm.Job('gatk_CatVCF-%s' % (bamfile.prefix))
job.memory = "10G"
job.output = util.File(os.path.join(outdir, vcfout))
job.append('gatk_catvcf.sh %s %s' % (job.output, ' '.join(vcfs)))
job.depend(*pjobs)
return job
def form_idr_inputs(name, sample):
os.makedirs(os.path.join(sample.results_dir, 'idr'))
jobs = []
for rep in sample.replicates + [sample.combined_replicate,]:
rep.narrowPeak = rep.unfiltered_results
rep.narrowPeak_pr1 = rep.unfiltered_results_pr1
rep.narrowPeak_pr2 = rep.unfiltered_results_pr2
sample.add_jobs(name, [sjm.Job('form_idr_inputs', ['echo form_idr_inputs',], queue=QUEUE, project=PROJECT, host='localhost',sched_options="-m e"),])
def merge_results(name, sample):
jobs = []
for r in sample.replicates + [sample.combined_replicate,]:
r.unfiltered_results = os.path.join(r.results_dir(sample), '%s_peaks.regionPeak' % r.rep_name(sample))
r.unfiltered_results_pr1 = os.path.join(r.pr1_results_dir, '%s_PR1_peaks.regionPeak' % r.rep_name(sample))
r.unfiltered_results_pr2 = os.path.join(r.pr2_results_dir, '%s_PR2_peaks.regionPeak' % r.rep_name(sample))
unpack_cmds = ['zcat %s > %s' % (r.spp_results, r.unfiltered_results), 'zcat %s > %s' % (r.spp_results_pr1, r.unfiltered_results_pr1), 'zcat %s > %s' % (r.spp_results_pr2, r.unfiltered_results_pr2),]
jobs.append(sjm.Job('merge_results_%s' % r.rep_name(sample), unpack_cmds, queue=QUEUE, project=PROJECT,sched_options="-m e"))
sample.add_jobs(name, jobs)
def form_idr_inputs(name, sample):
os.makedirs(os.path.join(sample.results_dir, 'idr'))
jobs = []
for rep in sample.replicates + [
sample.combined_replicate,
]:
cmds = []
rep.narrowPeak = rep.unfiltered_results + '.filtered'
cmd = 'sort -k8nr %s | head -n 300000 > %s.temp && mv %s.temp %s' % (
rep.unfiltered_results, rep.narrowPeak, rep.narrowPeak,
rep.narrowPeak)
cmds.append(cmd)
jobs.append(
sjm.Job(rep.rep_name(sample) + '_narrowPeak_filter',
cmds,
queue=QUEUE,
project=PROJECT))
# Pseudoreplicates
cmds = []
rep.narrowPeak_pr1 = rep.unfiltered_results_pr1 + '.filtered'
cmd = 'sort -k8nr %s | head -n 300000 > %s.temp && mv %s.temp %s' % (
rep.unfiltered_results_pr1, rep.narrowPeak_pr1, rep.narrowPeak_pr1,
rep.narrowPeak_pr1)
cmds.append(cmd)
jobs.append(
sjm.Job(rep.rep_name(sample) + '_PR1_narrowPeak_filter',
cmds,
queue=QUEUE,
project=PROJECT))
cmds = []
rep.narrowPeak_pr2 = rep.unfiltered_results_pr2 + '.filtered'
cmd = 'sort -k8nr %s | head -n 300000 > %s.temp && mv %s.temp %s' % (
rep.unfiltered_results_pr2, rep.narrowPeak_pr2, rep.narrowPeak_pr2,
rep.narrowPeak_pr2)
cmds.append(cmd)
jobs.append(
sjm.Job(rep.rep_name(sample) + '_PR2_narrowPeak_filter',
cmds,
queue=QUEUE,
project=PROJECT))
sample.add_jobs(name, jobs)
def gatk_joint(pjobs):
jobs = []
gvcfs = [pjob.output.path for pjob in pjobs]
outvcf = util.File(os.path.join(args.outdir, args.output))
job = sjm.Job('GATK-joint-gt-%s' % outvcf.name)
job.memory = "20G"
job.output = outvcf
job.append('gatk_gt_joint.sh %s %s' % (job.output, ' '.join(gvcfs)))
job.depend(*pjobs)
jobs.append(job)
return jobs
def idr_filter(name, sample):
cmd = os.path.join(BIN_DIR, 'idr_filter.py')
cmd += ' %s' % sample.run_name
cmd += ' %s' % sample.genome
cmd += ' %i' % len(sample.replicates)
cmd += ' %s' % sample.idr_dir
cmd += ' %s' % os.path.join(os.path.join(sample.results_dir, 'All'), sample.combined_replicate.unfiltered_results)
cmd += ' %s' % sample.results_dir
cmd += ' 7' # sort column (signal.value)
sample.add_jobs(name, [sjm.Job('idr_filter_' + sample.run_name, [cmd,], queue=QUEUE, project=PROJECT,sched_options="-m e"),])
def sam_flagstat(pjobs):
jobs = []
for pjob in pjobs:
bam=util.File(pjob.output)
job=sjm.Job('samtools-flagstat-%s' % bam.prefix)
job.memory = "10G"
job.output = bam.chext("flagstat.txt")
job.append('samtools flagstat %s > %s'%(bam, job.output))
job.depend(pjob)
jobs.append(job)
return jobs
def form_sample_files(name, sample):
jobs = []
print " peakseq: form sample files ***"
for rep in sample.replicates:
jobs.append(
sjm.Job(rep.rep_name(sample) + '_merge',
form_replicate_files(rep, sample),
queue=QUEUE,
modules=["samtools/1.2"],
project=PROJECT,
sched_options="-m e"))
jobs.append(
sjm.Job(sample.run_name + '_All_merge',
form_replicate_files(sample.combined_replicate, sample),
modules=["samtools/1.2"],
queue=QUEUE,
project=PROJECT,
sched_options="-m e"))
sample.add_jobs(name, jobs)
def archive_results(name, results_dir, archive_file, force=False):
if os.path.exists(archive_file):
if not force:
raise Exception("Archive file %s already exists" % archive_file)
archive_cmd = '%s %s %s %s' % (os.path.join(
BIN_DIR, 'archive_results.py'), results_dir, archive_file, force)
return sjm.Job('Archive_%s' % name,
archive_cmd,
queue=QUEUE,
project=PROJECT,
sched_options="-m e")
def dedup_bam(pjobs):
jobs = []
for pjob in pjobs:
bamfile = pjob.output
job = sjm.Job('picard_mdup-%s' % bamfile.prefix)
job.memory = "20G"
job.output = os.path.join(outdir, bamfile.chext("mdup.bam").name)
job.append('picard_mdup.sh %s %s' % (job.output, bamfile))
job.depend(pjob)
jobs.append(job)
return jobs
def split_species(pjobs):
jobs_mm9 = []
jobs_dm3 = []
for pjob in pjobs:
bamfile = pjob.output
job1 = sjm.Job('samtools_mm9-%s' % bamfile.prefix)
job1.memory = "12G"
job1.output = bamfile.chext('mm9.bam')
job1.append('samtools view -hb %s %s > %s' %
(bamfile, mm9_chrs, job1.output))
job1.depend(*pjobs)
jobs_mm9.append(job1)
job2 = sjm.Job('samtools_dm3-%s' % bamfile.prefix)
job2.memory = "12G"
job2.output = bamfile.chext('dm3.bam')
job2.append('samtools view -hb %s %s > %s' %
(bamfile, dm3_chrs, job2.output))
job2.depend(*pjobs)
jobs_dm3.append(job2)
return jobs_mm9, jobs_dm3
def dedup_merge(pjobs, outbam):
jobs = []
bams = []
for pjob in pjobs:
bams.append(pjob.output.path)
job = sjm.Job('picard_mdup-%s' % outbam )
job.memory = "20G"
job.output = util.File( os.path.join(outdir, outbam) )
job.append('picard_mdup.sh %s %s'%(job.output, ' '.join(bams) ) )
job.depend(*pjobs)
jobs.append(job)
return jobs
def gatk_recal(pjobs):
jobs = []
for pjob in pjobs:
bamfile = util.File(pjob.output)
job = sjm.Job('gatk_recalibrate-%s'%(bamfile.prefix))
job.memory = "20G"
job.output = os.path.join(tmpdir, '%s.%s' % (bamfile.prefix, 'recal.bam'))
job.regions = pjob.regions
job.append('gatk_recal.sh %s %s'%(job.output, bamfile.path))
job.depend(pjob)
jobs.append(job)
return jobs
def gatk_hc(pjobs):
jobs = []
for pjob in pjobs:
bamfile = util.File(pjob.output)
job = sjm.Job('gatk_haplotypecaller-%s'%(bamfile.prefix))
job.memory = "40G"
job.output = os.path.join(tmpdir, '%s.%s' % (bamfile.prefix, 'g.vcf.gz'))
job.regions = pjob.regions
job.append('gatk_hc.sh %s %s %s'%(job.output, bamfile.path, pjob.regions))
job.depend(pjob)
jobs.append(job)
return jobs
def gatk_gt(pjobs):
jobs = []
for pjob in pjobs:
gvcffile = util.File(pjob.output, iszipfile=True)
job = sjm.Job('gatk_genotypeGVCFs-%s'%(gvcffile.prefix))
job.memory = "15G"
job.output = os.path.join( tmpdir, '%s.%s' % (gvcffile.prefix, 'gt.vcf.gz') )
job.regions = pjob.regions
job.append('gatk_gt.sh %s %s %s'%(job.output, gvcffile.path, pjob.regions))
job.depend(pjob)
jobs.append(job)
return jobs
def merge_aln(pjobs):
jobs = []
for pjob in pjobs:
alnbam = pjob.output
ubam = pjob.input
job = sjm.Job('picard_mergeBam-%s' % alnbam.name)
job.memory = "10G"
job.output = util.File(alnbam.path.rstrip('.aln.bam') + '.sort.bam')
job.append('picard_mergeBam.sh %s %s %s' % (job.output, alnbam, ubam))
job.depend(pjob)
jobs.append(job)
return jobs
def gatk_hc_batch(bamfile, regions_file):
jobs = []
for region_line in open(args.regions_file):
region_line = region_line.rstrip('\n')
if region_line.startswith("#"): continue
region_name, regions = region_line.split(' ',1)
job = sjm.Job('gatk_hc_bam-%s-%s'%(bamfile.prefix, region_name))
job.memory = "40G"
job.output = os.path.join(tmpdir, '%s.%s.%s' % (bamfile.prefix, region_name,'g.vcf.gz'))
job.regions = regions
job.append('gatk_hc.sh %s %s %s'%(job.output, bamfile.path,regions))
jobs.append(job)
return jobs
def align_pe(pjobs):
jobs = []
for pjob in pjobs:
inbam = pjob.output
obam = inbam.chext('aln.bam')
job = sjm.Job('bwa_aln_pe-%s' % inbam.prefix)
job.memory = "20G"
job.input = inbam
job.output = obam
job.append('bwa_aln_pe_qn.sh %s %s %s' % (job.output, inbam, inbam))
job.depend(pjob)
jobs.append(job)
return jobs
def form_sample_files_nodups(name, sample):
jobs = []
for rep in sample.replicates:
jobs.append(
sjm.Job(rep.rep_name(sample) + '_merge',
form_replicate_files(rep, sample, rmdups=True),
modules=["samtools/1.2"],
queue=QUEUE,
project=PROJECT,
memory='16G',
sched_options="-m e"))
jobs.append(
sjm.Job(sample.run_name + '_All_merge',
form_replicate_files(sample.combined_replicate,
sample,
rmdups=True),
modules=["samtools/1.2"],
queue=QUEUE,
project=PROJECT,
memory='16G',
sched_options="-m e"))
sample.add_jobs(name, jobs)
def sort_ubam(ubams):
jobs = []
for ubam in ubams:
ubam = util.File(ubam)
obam = util.File(
os.path.join(tmpdir,
os.path.basename(ubam.path.rstrip('u.bam') + '.bam')))
job = sjm.Job('picard_sortUbam-%s' % ubam.prefix)
job.memory = "20G"
job.input = ubam
job.output = obam
job.append('picard_sortUbam.sh %s %s' % (job.input, job.output))
jobs.append(job)
return jobs
def align_se(reads1, reads2):
jobs = []
for i in range(0, len(reads1)):
read1 = reads1[i]
read2 = reads2[i]
readfile1 = util.File(read1)
readfile2 = util.File(read2)
bamname = re.sub(r'[._][Rr]1', '', readfile1.prefix) + '.sorted.bam'
bam = util.File(os.path.join(tmpdir, bamname))
job = sjm.Job('bwa_aln_se-%s' % readfile1.prefix)
job.output = bam
job.append('bwa_aln_se.sh %s %s %s %s' %
(job.output, read1, read2, readgroup))
jobs.append(job)
return jobs
def merge_bam(pjobs, out_prefix, suffix=None):
'''
Caveat: If output bam exists, needs to apply "-f" to overwrite or task will abort.
'''
bams = []
for pjob in pjobs:
bams.append(pjob.output.path)
job = sjm.Job('samtools_merge-%s' % suffix)
job.memory = "5G"
outname = os.path.join(tmpdir, '%s.%s.bam' % (out_prefix, suffix))
job.output = util.File(outname)
job.append('samtools merge %s %s && samtools index %s' %
(job.output, ' '.join(bams), job.output))
job.depend(*pjobs)
return job