Source code for modalysis.cli.parsers.gff

"""CLI parser registration for GFF command group."""

import argparse

from modalysis.cli.handlers.gff import handle_gff_annotate, handle_gff_format
from modalysis.constants import DEFAULT_PORT




def register_gff_parser(
    subparsers: argparse._SubParsersAction,
) -> None:
    """Register `gff` subcommands and arguments."""
    gff_parser = subparsers.add_parser("gff", help="GFF commands")
    gff_subparsers = gff_parser.add_subparsers(dest="gff_command")

    gff_format_parser = gff_subparsers.add_parser("format", help="Format a GFF file")
    gff_format_parser.add_argument(
        "--input-path", required=True, help="Path to the input GFF file"
    )
    gff_format_parser.add_argument(
        "--output-path", required=True, help="Path to the output directory"
    )
    gff_format_parser.add_argument(
        "--output-name", required=True, help="Name for the output file"
    )
    gff_format_parser.add_argument(
        "--allowed-chromosomes",
        required=True,
        help="Path to a file with one valid chromosome name per line",
    )
    gff_format_parser.add_argument(
        "--port",
        type=int,
        default=DEFAULT_PORT,
        help=f"Port the server is running on (default: {DEFAULT_PORT})",
    )
    gff_format_parser.set_defaults(func=handle_gff_format)

    gff_annotate_parser = gff_subparsers.add_parser(
        "annotate", help="Annotate formatted GFF file with expression data"
    )
    gff_annotate_parser.add_argument(
        "--gff-path",
        required=True,
        help="Path to the formatted GFF .modalysis file",
    )
    gff_annotate_parser.add_argument(
        "--expression-paths",
        required=True,
        nargs="+",
        help="Paths to expression TSV files",
    )
    gff_annotate_parser.add_argument(
        "--expression-labels",
        required=True,
        nargs="+",
        help="Labels for each expression file (must match order of --expression-paths)",
    )
    gff_annotate_parser.add_argument(
        "--output-path", required=True, help="Path to the output directory"
    )
    gff_annotate_parser.add_argument(
        "--output-name", required=True, help="Name for the output file"
    )
    gff_annotate_parser.add_argument(
        "--port",
        type=int,
        default=DEFAULT_PORT,
        help=f"Port the server is running on (default: {DEFAULT_PORT})",
    )
    gff_annotate_parser.set_defaults(func=handle_gff_annotate)