mergeFastqs.py 文件源码

def main():
    """
    Run main code

    1. Get arguments
    2. Setup logging
    3. Group filenames
    4. Merge files
    """

    args = get_args()

    setup_logging(args.outdir)
    logger = logging.getLogger("mergeFQs." + __name__)

    logger.info(str(len(args.fastqs)) + " input files provided")
    logger.info("Filename pattern is " + args.pattern)
    pattern = args.pattern.split(args.separator)
    ex_file = args.fastqs[0]
    ex_merge = merge_filename(ex_file, pattern, args.separator)
    logger.info("Example merge: " + ex_file + " -> " +
                os.path.join(args.outdir, ex_merge))
    file_groups = group_filenames(args.fastqs, pattern, args.separator)
    logger.info(str(len(file_groups)) + " file groups found...")
    merge_files(file_groups, args.outdir)