def main(args):
outbamfn = args.outBamFile
configReader = params.GetConfigReader()
params.InitConfigReader(args.configfile)
params.SetCancerType(args.cancerType)
params.SetOutputFileName(args.outBamFile)
params.SetSplitBamsPath(args.splitbams)
params.SetPhase(args.phase)
params.SetctDNA(args.ctDNA)
params.SetXY(args.singleXY)
params.SetCNV(args.cnvBed)
results_path = configReader.get('RESULTS', 'results_path')
cnvdir = "/".join([results_path, "cnv_dir"])
if (not os.path.exists(cnvdir)):
os.makedirs(cnvdir)
createEventBedFiles(cnvdir, params.GetCNV())
params.SetCNVDir(cnvdir)
# set software paths
java_path = bamhelp.GetJavaPath()
beagle_path = bamhelp.GetBeaglePath()
samtools_path = bamhelp.GetSamtoolsPath()
bedtools_path = bamhelp.GetBedtoolsPath()
vcftools_path = bamhelp.GetVCFtoolsPath()
sambamba_path = bamhelp.GetSambambaPath()
params.SetSoftwarePath(java_path, beagle_path, samtools_path,
bedtools_path, vcftools_path, sambamba_path)
if (args.phase):
run_pipeline(results_path)
else:
print('Please provide costume phasing algorithm')
def split_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 = []
prev_sentinels.append(taskHelpers.CreateFileList('None', -1,
sentinel_path))
split_path = "/".join([results_path, "splitbams"])
params.SetSplitBamsPath(split_path)
utils.createDirectory(split_path)
sentinels = taskHelpers.CreateFileList('{0}_split.sentinel', 1,
sentinel_path)
inputs.append(taskHelpers.CreateFileList('bam', 1, split_path + "/"))
outputs.append(
taskHelpers.CreateFileList('chr{1}.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 main(args):
outbamfn = args.outBamFile
configReader = params.GetConfigReader()
params.InitConfigReader(args.configfile)
params.SetGainCNV(args.cnvAmpFile)
params.SetLossCNV(args.cnvDelFile)
params.SetCancerType(args.cancerType)
params.SetOutputFileName(args.outBamFile)
params.SetSplitBamsPath(args.splitbams)
results_path = configReader.get('RESULTS', 'results_path')
#set software paths
java_path = bamhelp.GetJavaPath()
beagle_path = bamhelp.GetBeaglePath()
samtools_path = bamhelp.GetSamtoolsPath()
bedtools_path = bamhelp.GetBedtoolsPath()
vcftools_path = bamhelp.GetVCFtoolsPath()
sambamba_path = bamhelp.GetSambambaPath()
params.SetSoftwarePath(java_path, beagle_path, samtools_path,
bedtools_path, vcftools_path, sambamba_path)
if (args.phase):
run_pipeline(results_path)
verify_msg = infile_msg + '\n' + config_msg
pipelineHelpers.LogInputCheck(verify_msg)
if not (infile_pass and config_pass):
raise Exception('Invalid input.')
pipeline_msg = '\n---------------------------------\n' \
'Running pipeline\n' \
'---------------------------------'
print pipeline_msg
log = pipelineHelpers.GetLogFile('MAIN')
pipelineHelpers.Logging('INFO', log, pipeline_msg)
num_procs = line_count * 4
if( args.phase):
if(not args.splitbams):
pipeline_run([pipeline.find_roi_bam], multiprocess=num_procs, verbose=1)
if(args.cnvDelFile):
pipeline_run([pipeline.complete_pipeline])
else:
pipeline_run([pipeline.complete_pipeline_gain])
else:
params.SetSplitBamsPath(args.splitbams)
##to do
else:
print('user must provide phase VCFs') #user provides phased VCF
t1 = time.time()
def run_pipeline(results_path):
print(results_path)
global haplotype_path, cancer_dir_path, tmpbams_path, finalbams_path, log_path, logfile, terminating, logger, logQueue, res_path
res_path = results_path
haplotype_path, cancer_dir_path, tmpbams_path, finalbams_path, log_path, logfile = handle.GetProjectPaths(
results_path)
terminating, logger, logQueue = handle.GetLoggings(logfile)
chr_list = ['chr' + str(x) for x in range(1, 23)]
chr_list.extend(['chrX', 'chrY'])
t0 = time.time()
outbamfn = params.GetOutputFileName()
cnv_list = glob.glob("/".join([params.GetCNVDir(), '*.*']))
chromosome_event = create_chr_event_list(cnv_list, chr_list)
logger.debug('pipeline started!')
phase_path = '/'.join([results_path, 'phasedvcfdir'])
if not os.path.exists('/'.join([results_path, 'phasedvcfdir'])):
os.makedirs(phase_path)
initialize0(phase_path, cancer_dir_path)
for cnv_path in cnv_list:
initialize_pipeline(phase_path, haplotype_path, cnv_path)
pool1 = multiprocessing.Pool(
processes=12,
initializer=initPool,
initargs=[logQueue, logger.getEffectiveLevel(), terminating])
try:
if not params.GetSplitBamsPath():
if not os.path.exists("/".join([res_path, 'splitbams'])):
os.makedirs("/".join([res_path, 'splitbams']))
params.SetSplitBamsPath("/".join([res_path, 'splitbams']))
result0 = pool1.map_async(split_bam_by_chr,
chromosome_event).get(9999999)
result1 = pool1.map_async(find_roi_bam, chromosome_event).get(9999999)
result2 = pool1.map_async(implement_cnv, chromosome_event).get(9999999)
pool1.close()
except KeyboardInterrupt:
logger.debug('You cancelled the program!')
pool1.terminate()
except Exception as e:
logger.exception("Exception in main %s", e)
pool1.terminate()
finally:
pool1.join()
time.sleep(.1)
mergeSortBamFiles(outbamfn, finalbams_path)
t1 = time.time()
shutil.rmtree(tmpbams_path)
logger.debug(' ***** pipeline finished in ' +
str(round((t1 - t0) / 60.0, 1)) + ' minutes ***** ')
logging.shutdown()
