def repair_task_list():
"""main gain and loss algorithm"""
(sentinel_path, results_path, haplotype_path, cancer_dir_path,
tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
prev_sentinels.append(
taskHelpers.CreateFileList('{0}_findroi.sentinel', 1, sentinel_path))
sentinels = taskHelpers.CreateFileList('{0}_repair.sentinel', 1,
sentinel_path)
inputs.append(
taskHelpers.CreateFileList('{0}.{1}.roi.sorted.bam', 88, tmpbams_path,
"gain"))
outputs.append(
taskHelpers.CreateFileList('{0}.{1}.repaired.bam', 88, tmpbams_path,
"gain"))
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
def find_roi_bam_task_list():
"""populates task inputs and outputs"""
(sentinel_path, results_path, haplotype_path, cancer_dir_path,
tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
split_path = "/".join([results_path, "splitbams"])
prev_sentinels.append(
taskHelpers.CreateFileList('{0}_sortn.sentinel', 1, sentinel_path))
sentinels = taskHelpers.CreateFileList('{0}_findroi.sentinel', 1,
sentinel_path)
inputs.append(
taskHelpers.CreateFileList('{0}.byname.bam', 22, split_path,
"extractROI"))
outputs.append(
taskHelpers.CreateFileList('{0}.{1}.roi.bam', 88, tmpbams_path,
"extractROI")
) # max number of outputs chr*events*haplotypes (8 for 2 chromosomes)
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
def complete_pipeline_gain_task_list():
(sentinel_path, results_path, haplotype_path, cancer_dir_path,
tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
prev_sentinels.append(
taskHelpers.CreateFileList('{0}_subsample_gain.sentinel', 1,
sentinel_path))
sentinels = taskHelpers.CreateFileList('{0}_sortmerge.sentinel', 1,
sentinel_path)
inputs.append(
taskHelpers.CreateFileList('{0}_{1}_{2}.bam', 88, finalbams_path,
"FINAL"))
outputs.append(
taskHelpers.CreateFileList(params.GetOutputFileName(), 1,
finalbams_path))
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
def sort_by_name_task_list():
"""populates task inputs and outputs"""
(sentinel_path, results_path, haplotype_path, cancer_dir_path,
tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
split_path = "/".join([results_path, "splitbams"])
prev_sentinels.append(
taskHelpers.CreateFileList('{0}_split.sentinel', 1, sentinel_path))
sentinels = taskHelpers.CreateFileList('{0}_sortn.sentinel', 1,
sentinel_path)
inputs.append(
taskHelpers.CreateFileList('chr{1}.bam', 22, split_path + "/"))
outputs.append(
taskHelpers.CreateFileList('chr{1}.byname.bam', 22, split_path + "/"))
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
def subsample_loss_task_list():
(sentinel_path, results_path, haplotype_path, cancer_dir_path,
tmpbams_path, finalbams_path) = taskHelpers.GetProjectNamePathRunID()
inputs = []
outputs = []
prev_sentinels = []
prev_sentinels.append(
taskHelpers.CreateFileList('{0}_mutate_loss.sentinel', 1,
sentinel_path))
sentinels = taskHelpers.CreateFileList('{0}_subsample_loss.sentinel', 1,
sentinel_path)
inputs.append(
taskHelpers.CreateFileList('{0}.{1}.mutated.merged.sorted.bam', 12,
tmpbams_path, "loss"))
outputs.append(
taskHelpers.CreateFileList('{0}{1}_GAIN.bam', 88, tmpbams_path,
"loss"))
sample_ids = taskHelpers.CreateFileList('{0}', 1, '')
job_parameters = taskHelpers.CreateTaskList(inputs, sentinels, outputs,
sample_ids, prev_sentinels)
for job in job_parameters:
yield job
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 mutate_loss(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, 'loss_het_snp_' + chr + '.bed'])
diffn = "/".join([tmpbams_path,"diff.bam"])
nonhet= "/".join([tmpbams_path, 'diff_only1_' + os.path.basename(inp)])
hetfn=sub('.roi.sorted.bam$',".mutated.het.bam", inp)
hetfnsorted = sub('.roi.sorted.bam$',".mutated.het.sorted.bam", inp)
mergedsortfn = sub('.roi.sorted.bam$',".mutated.merged.sorted.bam", inp)
script = open('{0}mutate_{1}_{2}.sh'.format(script_path, chr, "loss"), 'w')
script.write('#!/bin/bash\n')
script.write('#')
script.write('#$ -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 {inp1} {bf} {happath}\n\n'.format(inp1=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.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')
import itertools
import re
import subprocess
global bases
bases = ('A','T','C','G')
log = pipelineHelpers.GetLogFile('Bamgineer')
import utils
import vcf
import gzip
import shutil
chr_list = range(1,23)
event_list=['gain','loss']
sentinel_path, results_path,haplotype_path,cancer_dir_path,tmpbams_path,finalbams_path = taskHelpers.GetProjectNamePathRunID()
def initPool(queue, level, terminating_):
"""
This causes the logging module to be initialized with the necessary info
in pool threads to work correctly.
"""
logging.getLogger('').setLevel(level)
global terminating
terminating = terminating_
def initialize():
try:
utils.createDirectory(results_path)
