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()