blocks = explogparser.getBlocksFromExpLogJson(env['exp_json'], excludeThumbnail=True) dirs = ['block_%s' % block['id_str'] for block in blocks] if not is_composite: dirs=[] if args.do_sigproc: set_result_status('Merge Heatmaps') exclusionMaskFile = 'exclusionMask_%s.txt' % env.get('chipType','').lower() sigproc.mergeSigProcResults( dirs, env['SIGPROC_RESULTS'], env['shortRunName'], exclusionMaskFile) if args.do_basecalling: set_result_status('Merge Basecaller Results') # write composite return code try: composite_return_code=96 for subdir in dirs: blockstatus_return_code_file = os.path.join(subdir,"blockstatus.txt") if os.path.exists(blockstatus_return_code_file):
number_of_total_blocks = len(blocks_to_process) dirs = ["block_%s" % block["id_str"] for block in blocks_to_process] if not is_composite: dirs = [] if args.do_sigproc: set_result_status("Merge Heatmaps") # In 5.4 we apply a mask in the bead find stage but also here to be backward compatible # with from-basecall reanalyses of 5.2 and older OIA results exclusionMaskFile = "exclusionMask_%s.txt" % env.get("chipType", "").lower() sigproc.mergeSigProcResults(dirs, env["SIGPROC_RESULTS"], env["shortRunName"], exclusionMaskFile) """ # write composite return code, not needed anymore ? try: composite_return_code=number_of_total_blocks for subdir in dirs: blockstatus_return_code_file = os.path.join(subdir,"blockstatus.txt") if os.path.exists(blockstatus_return_code_file): with open(blockstatus_return_code_file, 'r') as f: text = f.read() if 'Analysis=0' in text: composite_return_code-=1 composite_return_code_file = os.path.join(SIGPROC_RESULTS,"analysis_return_code.txt")
printtime("MergeTLStatus %s\tpid %d\tpk file %s started" % (status, os.getpid(), primary_key_file)) except: traceback.print_exc() blocks = explogparser.getBlocksFromExpLogJson(env['exp_json'], excludeThumbnail=True) dirs = ['block_%s' % block['id_str'] for block in blocks] if args.do_sigproc: set_result_status('Merge Heatmaps') merged_bead_mask_path = os.path.join(env['SIGPROC_RESULTS'], 'MaskBead.mask') sigproc.mergeSigProcResults(dirs, env['SIGPROC_RESULTS'], env['shortRunName']) if args.do_basecalling: set_result_status('Merge Basecaller Results') try: sigproc.mergeRawPeakSignals(dirs) except: traceback.print_exc() try: # Only merge metrics and generate plots basecaller.merge_basecaller_stats(dirs, env['BASECALLER_RESULTS'], env['SIGPROC_RESULTS'], env['flows'], env['flowOrder'])
number_of_total_blocks = len(blocks_to_process) dirs = ['block_%s' % block['id_str'] for block in blocks_to_process] if not is_composite: dirs = [] if args.do_sigproc: set_result_status('Merge Heatmaps') # In 5.4 we apply a mask in the bead find stage but also here to be backward compatible # with from-basecall reanalyses of 5.2 and older OIA results exclusionMaskFile = 'exclusionMask_%s.txt' % env.get('chipType', '').lower() sigproc.mergeSigProcResults( dirs, env['SIGPROC_RESULTS'], env['shortRunName'], exclusionMaskFile) ''' # write composite return code, not needed anymore ? try: composite_return_code=number_of_total_blocks for subdir in dirs: blockstatus_return_code_file = os.path.join(subdir,"blockstatus.txt") if os.path.exists(blockstatus_return_code_file): with open(blockstatus_return_code_file, 'r') as f: text = f.read() if 'Analysis=0' in text:
env,warn = explogparser.getparameter() blockprocessing.write_version() sys.stdout.flush() sys.stderr.flush() blocks = explogparser.getBlocksFromExpLogJson(env['exp_json'], excludeThumbnail=True) dirs = ['block_%s' % block['id_str'] for block in blocks] if args.do_sigproc: merged_bead_mask_path = os.path.join(env['SIGPROC_RESULTS'], 'MaskBead.mask') sigproc.mergeSigProcResults( dirs, env['SIGPROC_RESULTS'], env['shortRunName']) if args.do_basecalling: # Only merge metrics and generate plots basecaller.merge_basecaller_stats( dirs, env['BASECALLER_RESULTS'], env['SIGPROC_RESULTS'], env['flows'], env['flowOrder']) ## Generate BaseCaller's composite "Big Data": unmapped.bam. Totally optional if env.get('libraryName','') == 'none': actually_merge_unmapped_bams = True else:
blockprocessing.printheader() env = blockprocessing.getparameter() blockprocessing.write_version() sys.stdout.flush() sys.stderr.flush() blocks = blockprocessing.getBlocksFromExpLog(env['exp_json'], excludeThumbnail=True) dirs = ['block_%s' % block['id_str'] for block in blocks] if args.do_sigproc: sigproc.mergeSigProcResults( dirs, env['pathToRaw'], env['skipchecksum'], env['SIGPROC_RESULTS']) if args.do_basecalling: QualityPath = os.path.join(env['BASECALLER_RESULTS'], 'quality.summary') libsff = "%s/%s_%s.sff" % (env['BASECALLER_RESULTS'], env['expName'], env['resultsName']) tfsff = "%s/%s_%s.tf.sff" % (env['BASECALLER_RESULTS'], env['expName'], env['resultsName']) merged_bead_mask_path = os.path.join(env['SIGPROC_RESULTS'], 'MaskBead.mask') basecaller.mergeBasecallerResults( dirs, QualityPath,