modules.cli

  1import argparse
  2
  3'''
  4cli.py, handles argument parsing
  5'''
  6
  7def build_parser() -> argparse.ArgumentParser:
  8    '''
  9    Build CLI arg parser for the main script
 10
 11    Args:
 12        None
 13
 14    Outputs:
 15        argparse.ArgumentParser: parser object
 16    '''
 17    parser = argparse.ArgumentParser(
 18        prog="Slipper",
 19        description='''
 20        Extract soft clipped bases from BAM. For output description see repo's
 21        README.md
 22        ''', epilog="M.Hryc (2025)"
 23    )
 24
 25    subparsers = parser.add_subparsers(dest='command')
 26
 27    # === the 'extract' subcommand ===
 28
 29    extract = subparsers.add_parser(
 30        "extract", help='''
 31        Extract soft clipped bases from BAM
 32        '''
 33    )
 34    extract.add_argument(
 35        "-i", "--input",
 36        required=True,
 37        type=str, help='''
 38    Path to the input BAM file (needs an index)'''
 39    )
 40    extract.add_argument(
 41        "-o", "--output",
 42        required=True,
 43        type=str, help='''
 44    Path to the output file (without file extensions)'''
 45    )
 46    extract.add_argument(
 47        "-g", "--gzip",
 48        action="store_true",
 49        help='''
 50    Output to gzip compressed file'''
 51    )
 52    extract.add_argument(
 53        "-c", "--compress-level", metavar="LEVEL",
 54        required=False, default=1, type=int,
 55        help='''
 56    Gzip compression level (default=2)'''
 57    )
 58    extract.add_argument(
 59        "-s", "--with-sequence",
 60        required=False, action="store_true",
 61        help='''
 62    Store the whole read sequence (SEQ) in the last column. Default is off
 63    (fill with "NA")'''
 64    )
 65
 66    # === the 'analyse' subcommand
 67
 68    analyse = subparsers.add_parser(
 69        "analyse", help='''
 70        Analyse the output of 'Slipper extract'
 71        '''
 72    )
 73    analyse.add_argument(
 74        "-i", "--input",
 75        required=True,
 76        type=str, help='''
 77        Path to the input TSV produced by 'Slipper extract'
 78        '''
 79    )
 80    analyse.add_argument(
 81        "--short-output", action="store_true",
 82        help='''
 83        Skip the lines with 'no_tail' in the output
 84        '''
 85    )
 86    analyse.add_argument(
 87        "-o", "--output",
 88        required=True,
 89        type=str, help='''
 90        Path to the output file (without file extensions)
 91        '''
 92    )
 93
 94    # === the 'plot' subcommand ===
 95
 96    plot = subparsers.add_parser(
 97        "plot", help='''
 98        Make plots from 'Slipper analyse' output
 99        '''
100    )
101    plot.add_argument(
102        "-i", "--input",
103        required=True, type=str, 
104        nargs='+', help='''
105        Path to the input TSVs produced by 'Slipper analyse'
106        '''
107    )
108    plot.add_argument(
109        "-o", "--outdir",
110        default="slipper_plots",
111        type=str, help='''
112        Path to directory, where plots will be saved. Defaults to slipper_plots/
113        '''
114    )
115
116    return parser