slipper 

 1#!/usr/bin/env python3
 2
 3from modules.cli import build_parser
 4from modules.extract import extractor
 5from modules.analyse import analyser
 6from modules.plot import ploter
 7
 8# === Main logic ===
 9
10def main() -> None:
11    '''
12    Main function. Builds arg parser with cli module. Runs a submodule based on
13    passed subcommand.
14    '''
15    # build parser and parse args
16    parser = build_parser()
17    args = parser.parse_args()
18
19    if args.command == "extract":
20        extractor(in_bam=args.input,
21                  out_name=args.output,
22                  seq_switch=args.with_sequence,
23                  gzip_switch=args.gzip,
24                  gzip_level=args.compress_level)
25
26    elif args.command == "analyse":
27        analyser(args.input,
28                 out_name=args.output,
29                 briefmode=args.short_output)
30    
31    elif args.command == "plot":
32        ploter(infiles=args.input)
33
34    return None
35
36if __name__ == "__main__":
37    main()
def main() -> None: 
11def main() -> None:
12    '''
13    Main function. Builds arg parser with cli module. Runs a submodule based on
14    passed subcommand.
15    '''
16    # build parser and parse args
17    parser = build_parser()
18    args = parser.parse_args()
19
20    if args.command == "extract":
21        extractor(in_bam=args.input,
22                  out_name=args.output,
23                  seq_switch=args.with_sequence,
24                  gzip_switch=args.gzip,
25                  gzip_level=args.compress_level)
26
27    elif args.command == "analyse":
28        analyser(args.input,
29                 out_name=args.output,
30                 briefmode=args.short_output)
31    
32    elif args.command == "plot":
33        ploter(infiles=args.input)
34
35    return None

Main function. Builds arg parser with cli module. Runs a submodule based on passed subcommand.