def subsample_loss(inputs, output_sentinel, outputs, sample_id, prev_sentinel):
"""adjusting sample rate for Bam files"""
task_list = []
log_msg = ' [subsample loss events] ' + '[' + sample_id + '] '
if pipelineHelpers.CheckSentinel(prev_sentinel, log, log_msg):
pipelineHelpers.Logging('INFO', log, log_msg + 'Starting')
python = sys.executable
current_path = params.GetProgramPath()
script_path = pipelineHelpers.GetScriptPath(
sample_id, bamhelp.name)
bamgineer_mem = bamhelp.GetBamgineerMem('med')
for inp in inputs[0]:
chrevent=os.path.basename(inp).strip().split("_")[0]
chr = re.split('(\d+)',chrevent)[1]
original_bam = sub('.mutated.merged.sorted.bam', '.sorted.bam', inp)
sentinel_path, results_path,haplotype_path,cancer_dir_path,tmpbams_path,finalbams_path = taskHelpers.GetProjectNamePathRunID()
LOSS_FINAL = "/".join([finalbams_path, 'CHR'+str(chr).upper() +'_LOSS.bam'])
script = open('{0}sample_{1}_{2}.sh'.format(script_path, 'chr'+str(chr), "loss"), 'w')
script.write('#!/bin/bash\n')
script.write('#\n')
script.write('#$ -cwd \n')
script.write('module load samtools/1.2 \n')
script.write('python {path}/subsample_loss.py {inbam} {fl} \n'.format(path=current_path,inbam=inp, fl=LOSS_FINAL))
script.close()
process = pipelineHelpers.RunTask(
os.path.abspath(script.name),4, bamgineer_mem,
sample_id, bamhelp.name)
task_list.append(process)
pipelineHelpers.CheckTaskStatus(
task_list, output_sentinel, log, log_msg)
pipelineHelpers.Logging('INFO', log, log_msg+ 'Finished Sampling Loss Event')
def complete_pipeline(inputs, output_sentinel, outputs, sample_id, prev_sentinel):
"""merge, sort, clean up """
task_list = []
log_msg = ' [Final merge] ' + '[' + sample_id + '] '
pipelineHelpers.Logging('INFO', log, log_msg + 'Starting')
if pipelineHelpers.CheckSentinel(prev_sentinel, log, log_msg):
python = sys.executable
current_path = params.GetProgramPath()
script_path = pipelineHelpers.GetScriptPath(
sample_id, bamhelp.name)
bamgineer_mem = bamhelp.GetBamgineerMem('high')
mergedbamname = params.GetOutputFileName()
script = open('{0}mergesort.sh'.format(script_path), 'w')
script.write('#!/bin/bash\n')
script.write('#\n')
script.write('#$ -cwd \n')
script.write('module load sambamba \n')
script.write('python {path}/mergesort.py '
' {mergedfinal} {finalbamdir}\n'.format(path=current_path, mergedfinal=mergedbamname, finalbamdir=finalbams_path))
script.close()
process = pipelineHelpers.RunTask( os.path.abspath(script.name), 4, bamgineer_mem,
sample_id, bamhelp.name)
task_list.append(process)
pipelineHelpers.CheckTaskStatus(
task_list, output_sentinel, log, log_msg)
pipelineHelpers.Logging('INFO', log, log_msg + 'COMPLETE!')
def repair_gain( inputs, output_sentinel, outputs, sample_id, prev_sentinel):
"""implementing cnv module and finding reads not matching hg19 at germline SNP locations"""
task_list = []
log_msg = ' [re-pairing reads] ' + '[' + sample_id + '] '
pipelineHelpers.Logging('INFO', log, log_msg + 'Starting')
if pipelineHelpers.CheckSentinel(prev_sentinel, log, log_msg):
python = sys.executable
current_path = params.GetProgramPath()
script_path = pipelineHelpers.GetScriptPath(
sample_id, bamhelp.name)
bamgineer_mem = bamhelp.GetBamgineerMem('med')
for inp in inputs[0]:
chr= os.path.basename(inp).strip().split(".")[0]
script = open('{0}re-pair_{1}_{2}.sh'.format(script_path, chr, "gain"), 'w')
script.write('#!/bin/bash\n\n')
script.write('module load samtools/1.2 \n')
script.write('module load sambamba \n')
script.write('python {path}/re-pair.py {inbam} \n'.format(inbam=inp, path=current_path ))
script.close()
process = pipelineHelpers.RunTask(
os.path.abspath(script.name),4, bamgineer_mem,
sample_id, bamhelp.name)
task_list.append(process)
pipelineHelpers.CheckTaskStatus(
task_list, output_sentinel, log, log_msg)
pipelineHelpers.Logging('INFO', log, log_msg + 'Finished Re-pairing')
def sort_by_name(inputs, output_sentinel, outputs, sample_id, prev_sentinel):
"""sorting bam file by name"""
task_list = []
log_msg = ' [SortByName] ' + '[' + sample_id + '] '
pipelineHelpers.Logging('INFO', log, log_msg + 'Starting')
if pipelineHelpers.CheckSentinel(prev_sentinel, log, log_msg):
python = sys.executable
script_path = pipelineHelpers.GetScriptPath(
sample_id, bamhelp.name)
bamgineer_mem = bamhelp.GetBamgineerMem('med')
for outp, inp, num in zip( outputs[0], inputs[0], chr_list):
script = open(
'{0}sortbyname_chr{1}.sh'.format(script_path,
num), 'w')
script.write('#!/bin/bash\n')
script.write('#\n')
script.write('#$ -cwd \n')
script.write('module load sambamba \n')
script.write('sambamba sort -n {inp} '
'-o {outp} -t 4 \n'.format(inp = inp, outp=outp))
script.close()
process = pipelineHelpers.RunTask(
os.path.abspath(script.name), 4, bamgineer_mem,
sample_id, bamhelp.name)
task_list.append(process)
pipelineHelpers.CheckTaskStatus(
task_list, output_sentinel, log, log_msg)
pipelineHelpers.Logging('INFO', log, log_msg + 'Finished SplitBams')
def mutate_gain(inputs, output_sentinel, outputs, sample_id, prev_sentinel):
"""mutating reads according to haplotype at germline SNP locations"""
task_list = []
log_msg = ' [implement_cnv] ' + '[' + sample_id + '] '
if pipelineHelpers.CheckSentinel(prev_sentinel, log, log_msg):
pipelineHelpers.Logging('INFO', log, log_msg + 'Starting')
python = sys.executable
current_path = params.GetProgramPath()
script_path = pipelineHelpers.GetScriptPath(
sample_id, bamhelp.name)
bamgineer_mem = bamhelp.GetBamgineerMem('med')
sentinel_path, results_path,haplotype_path,cancer_dir_path,tmpbams_path,finalbams_path = taskHelpers.GetProjectNamePathRunID()
for inp in inputs[0]:
chr= os.path.basename(inp).strip().split(".")[0]
bedfn= "/".join([haplotype_path, 'gain_het_snp_' + chr + '.bed'])
diffn = "/".join([tmpbams_path,"diff.bam"])
nonhet= "/".join([tmpbams_path, 'diff_only1_' + os.path.basename(inp)])
hetfn=sub('.gain.roi.repaired.sorted.bam$','.gain.mutated.het.bam', inp)
hetfnsorted = sub('.gain.roi.repaired.sorted.bam$','.gain.mutated.het.sorted.bam', inp)
mergedsortfn = sub('.gain.roi.repaired.sorted.bam$','.gain.mutated.merged.sorted.bam', inp)
mergedrenamedfn = sub('.gain.roi.repaired.sorted.bam$','.gain.renamed.mutated.merged.sorted.bam', inp)
script = open('{0}mutate_{1}_{2}.sh'.format(script_path, chr, "gain"), 'w')
script.write('#!/bin/bash\n')
script.write('#')
script.write('#$ -cwd \n')
script.write('module load samtools/1.2 \n')
script.write('module load sambamba \n')
script.write('module load bamUtil \n')
script.write('sort -u {bf} -o {bf}\n\n'.format(bf=bedfn))
script.write('python {path}/mutate.py {repairedbam} {bf} {happath}\n\n'.format(repairedbam=inp, bf=bedfn ,path=current_path , happath=haplotype_path))
script.write('sambamba sort {het} -o {hetsort}\n\n'.format(het=hetfn, hetsort=hetfnsorted))
script.write('bam diff --in1 {repairedbam} --in2 {hetsort} --out {dif}\n\n'.format(repairedbam=inp, hetsort=hetfnsorted ,dif=diffn ))
script.write('sambamba merge {merged} {hetonly} {nonhetonly}\n\n'.format(merged=mergedsortfn,hetonly=hetfnsorted, nonhetonly= nonhet))
script.write('rm {het} {nonhetonly} \n\n'.format(het=hetfn,nonhetonly= nonhet))
script.write('python {path}/rename-reads.py {inp2} {outp}\n\n'.format(inp2= mergedsortfn, outp=mergedrenamedfn, path=current_path))
script.close()
process = pipelineHelpers.RunTask(
os.path.abspath(script.name),4, bamgineer_mem,
sample_id, bamhelp.name)
task_list.append(process)
pipelineHelpers.CheckTaskStatus(
task_list, output_sentinel, log, log_msg)
pipelineHelpers.Logging('INFO', log, log_msg + 'Finished Mutating')
def find_roi_bam(inputs, output_sentinel, outputs, sample_id, prev_sentinel):
"""finding ROI bam for each haplotype/event/chr"""
task_list = []
log_msg = ' [FindRoiBam] ' + '[' + sample_id + '] '
pipelineHelpers.Logging('INFO', log, log_msg + 'Starting')
if pipelineHelpers.CheckSentinel(prev_sentinel, log, log_msg):
python = sys.executable
script_path = pipelineHelpers.GetScriptPath(sample_id, bamhelp.name)
bamgineer_mem = bamhelp.GetBamgineerMem('med')
sentinel_path, results_path, haplotype_path, cancer_dir_path, tmpbams_path, finalbams_path = taskHelpers.GetProjectNamePathRunID(
)
for inp, op in izip(inputs[0], outputs[0]):
opsorted = sub('.bam$', ".sorted.bam", op)
chr = os.path.basename(op).strip().split(".")[0]
event = os.path.basename(op).strip().split(".")[1]
exonsinroibed = "/".join(
[haplotype_path, event + "_exons_in_roi_" + str(chr) + '.bed'])
script = open(
'{0}find_roi_{1}_{2}.sh'.format(script_path, chr, event), 'w')
script.write('#!/bin/bash\n\n')
script.write('#\n')
script.write('#$ -cwd \n')
script.write('module load bedtools \n')
script.write('module load sambamba \n')
script.write('sort -u {exonbed} -o {exonbed} \n'.format(
exonbed=exonsinroibed))
script.write('bedtools pairtobed -abam {inp} '
'-b {bf} -type either > {outp} \n'.format(
inp=inp, bf=exonsinroibed, outp=op))
script.write('sambamba sort {outp} -o '
'{outpsorted} \n'.format(outp=op,
outpsorted=opsorted))
script.write('rm {outp} \n'.format(outp=op))
script.close()
process = pipelineHelpers.RunTask(os.path.abspath(script.name), 1,
bamgineer_mem, sample_id,
bamhelp.name)
task_list.append(process)
pipelineHelpers.CheckTaskStatus(task_list, output_sentinel, log,
log_msg)
pipelineHelpers.Logging('INFO', log, log_msg + 'Finished FindROI')
def split_bams(inputs, output_sentinel, outputs, sample_id, prev_sentinel):
"""splits bam according to chromosome"""
task_list = []
log_msg = ' [SplitBams] ' + '[' + sample_id + '] '
pipelineHelpers.Logging('INFO', log, log_msg + 'Starting')
if pipelineHelpers.CheckSentinel(prev_sentinel, log, log_msg):
python = sys.executable
script_path = pipelineHelpers.GetScriptPath(
sample_id, bamhelp.name)
bamgineer_mem = bamhelp.GetBamgineerMem('med')
exons = params.GetExonPath()
command= "".join(["""awk '($1 ~ "chr"){print $0 >> $1".bed" }' """, exons])
initialize()
os.chdir(script_path)
#utils.runCommand(command)
for outp, num in zip(outputs[0], chr_list):
script = open(
'{0}splitbam_chr{1}.sh'.format(script_path,
num), 'w')
script.write('#!/bin/bash\n')
script.write('#\n')
script.write('#$ -cwd \n')
script.write('module load samtools \n')
script.write(command +'\n')
script.write('samtools view -bh {bam} chr{num} > '
'{out}\n'.format(bam=inputs[0][0],
num=num, out=outp))
script.close()
process = pipelineHelpers.RunTask(
os.path.abspath(script.name), 4, bamgineer_mem,
sample_id, bamhelp.name)
task_list.append(process)
pipelineHelpers.CheckTaskStatus(
task_list, output_sentinel, log, log_msg)
pipelineHelpers.Logging('INFO', log, log_msg + 'Finished task1')