fast5_to_fastq.py 文件源码

def get_arguments():
    parser = argparse.ArgumentParser(description='FAST5 to FASTQ',
                                     formatter_class=argparse.ArgumentDefaultsHelpFormatter)
    parser.add_argument('dir', type=str,
                        help='directory of FAST5 reads to extract (will be searched recursively)')
    parser.add_argument('--min_length', type=int, default=0,
                        help='Exclude reads shorter than this length (in bp)')
    parser.add_argument('--min_mean_qual', type=float, default=0.0,
                        help='Exclude reads with a mean qscore less than this value')
    parser.add_argument('--min_qual_window', type=float, default=0.0,
                        help='Exclude reads where their mean qscore in a sliding window drops '
                             'below this value')
    parser.add_argument('--window_size', type=int, default=50,
                        help='The size of the sliding window used for --min_qual_window')
    parser.add_argument('--target_bases', type=int, default=None,
                        help='If set, exclude the worst reads (as judged by their minimum qscore '
                             'in a sliding window) such that only this many bases remain')
    args = parser.parse_args()
    args.dir = os.path.abspath(args.dir)
    return args