def GetBlocksToAnalyze(env): blocks = [] if is_thumbnail or is_wholechip: block = {"id_str": "", "datasubdir": "", "jobcmd": [], "jobid": None, "status": None} base_args = env["analysisArgs"].strip().split(" ") base_args.append("--libraryKey=%s" % env["libraryKey"]) base_args.append("--tfKey=%s" % env["tfKey"]) base_args.append("--no-subdir --wellsfileonly") if is_thumbnail: thumbnailsize = blockprocessing.getThumbnailSize(env["exp_json"]) block["id_str"] = "thumbnail" base_args.append("--cfiedr-regions-size=50x50") base_args.append("--block-size=%sx%s" % (thumbnailsize[0], thumbnailsize[1])) base_args.append("--beadfind-thumbnail 1") base_args.append("--bkg-debug-param 1") elif is_wholechip: block["id_str"] = "wholechip" base_args.append("--output-dir=%s" % env["SIGPROC_RESULTS"]) block["jobcmd"] = base_args print base_args print block blocks.append(block) else: explogblocks = blockprocessing.getBlocksFromExpLog(env["exp_json"]) for block in explogblocks: # ignore thumbnail if block["id_str"] == "thumbnail": continue base_args = env["analysisArgs"].strip().split(" ") # raw data dir is last element in analysisArgs and needs the block subdirectory appended base_args[-1] = os.path.join(base_args[-1], block["datasubdir"]) rawDirectory = base_args[-1] base_args.append("--libraryKey=%s" % env["libraryKey"]) base_args.append("--no-subdir --wellsfileonly") base_args.append("--output-dir=%s" % env["SIGPROC_RESULTS"]) block["jobcmd"] = base_args print "expblock: " + str(block) if (block["autoanalyze"] and block["analyzeearly"]) or os.path.isdir(rawDirectory): print "base_args: " + str(base_args) print "block: " + str(block) blocks.append(block) return blocks
if args.verbose: print "MergeTLScript:",args if not args.do_sigproc and not args.do_basecalling and not args.do_alignment and not args.do_zipping: parser.print_help() sys.exit(1) 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: