def main(): #initialize the logging utils_logging.init_logging(logging.INFO) #Setup options optparser=_prepare_optparser() (options,args) = optparser.parse_args() #verify options arg_pass=_verifyOption(options) if not arg_pass: logging.warning(optparser.get_usage()) logging.critical("Non valid arguments: exit") sys.exit(1) if options.debug: utils_logging.init_logging(logging.DEBUG) utils_logging.init_logging(output_level=None, log_file_name=os.path.join(options.output_dir,"extract_and_assemble.log")) bam_files=[options.bam_files] if len(args)>0: bam_files.extend(args) all_assembler_to_try = options.assembler_name.split(',') assembly_function_list=[] for assembler_name in all_assembler_to_try: assembly_function=RAD_assemble_read2.get_assembly_function(assembler_name) assembly_function_list.append(assembly_function) command_runner.set_command_to_run_localy() if options.rg_ids: rg_ids=options.rg_ids.split() else: rg_ids=[] extract_and_assemble(bam_files, options.read1_consensus_file, options.white_list_file, options.output_dir, assembly_function_list, subsample_nb_read=options.subsample_nb_read, rg_ids=rg_ids, adapter_file=options.adapter_file)