Source code for modalysis.cli.parsers

"""Top-level CLI parser construction."""

import argparse

from modalysis.cli.parsers.dmr import register_dmr_parser
from modalysis.cli.parsers.gff import register_gff_parser
from modalysis.cli.parsers.pileup import register_pileup_parser
from modalysis.cli.parsers.plot import register_plot_parser
from modalysis.cli.parsers.server import register_server_parser




[docs]
def build_parser() -> argparse.ArgumentParser:
    """Build and return the root argparse parser for modalysis CLI."""
    parser = argparse.ArgumentParser(
        prog="modalysis", description="Methylation and DMR Analysis"
    )
    parser.add_argument(
        "-v", "--verbose", action="store_true", help="Enable debug logging"
    )
    subparsers = parser.add_subparsers(dest="command")

    register_server_parser(subparsers)
    register_dmr_parser(subparsers)
    register_gff_parser(subparsers)
    register_pileup_parser(subparsers)
    register_plot_parser(subparsers)

    return parser