def run_pipeline(results_path):
global haplotype_path,cancer_dir_path,tmpbams_path, finalbams_path,log_path, logfile ,terminating,logger,logQueue
haplotype_path,cancer_dir_path,tmpbams_path, finalbams_path,log_path, logfile = handle.GetProjectPaths(results_path)
terminating,logger,logQueue = handle.GetLoggings(logfile)
t0 = time.time()
outbamfn=params.GetOutputFileName()
chromosome_event = create_chr_event_list()
chromosomes_bamfiles = create_chr_bam_list()
logger.debug('pipeline started!')
initialize(results_path,haplotype_path,cancer_dir_path)
pool1 = multiprocessing.Pool(processes=4, initializer=initPool, initargs=[logQueue, logger.getEffectiveLevel(), terminating] )
try:
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()
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()