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 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 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 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')
import os
import sys
from re import sub
from ruffus import *
from helpers import depthOfCoverageTasks, depthOfCoverageHelpers, pipelineHelpers
from helpers import runIDHelpers as rid
from helpers import parameters as params
import subprocess
current_path = params.GetProgramPath()
log = pipelineHelpers.GetLogFile('DepthOfCoverage')
def runCommand(cmd):
try:
process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stdin=subprocess.PIPE, shell=True)
stdout, stderr = process.communicate()
except OSError as e:
print("Execution failed:", e)