alignStats.py 文件源码

def main():
    """
    Main function.

    1. Setup logging
    2. Get arguments
    3. Get index
    4. Process files
    5. Write output
    """

    setup_logging()

    logger = logging.getLogger("stats." + __name__)

    args = get_args()

    index = get_index(args)

    logger.warning("Positions not in annotation will be ignored.")

    logger.info("Found " + str(len(args.inputs)) + " input file(s):")
    for input_file in sorted(args.inputs):
        logger.debug(input_file)

    if args.is_parallel:
        stats = Parallel(n_jobs=args.parallel,
                         verbose=100,
                         batch_size=1)(delayed(process_file)(input_file,
                                                             args.type,
                                                             index,
                                                             args.is_parallel)
                                       for input_file in args.inputs)
    else:
        stats = []
        for input_file in args.inputs:
            output_table = process_file(input_file, args.type, index,
                                        args.is_parallel)
            stats.append(output_table)

    write_stats(args.out, stats)