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)
