Source code for modalysis.cli.handlers.gff

"""CLI handlers for GFF commands."""

import argparse
import logging

from modalysis.client.gff import gff_annotate, gff_format

logger = logging.getLogger(__name__)




def handle_gff_format(args: argparse.Namespace) -> None:
    """Handle `modalysis gff format` CLI command."""
    with open(args.allowed_chromosomes) as f:
        allowed_chromosomes = [line.strip() for line in f if line.strip()]
    base_url = f"http://localhost:{args.port}"
    result = gff_format(
        input_path=args.input_path,
        output_path=args.output_path,
        output_name=args.output_name,
        allowed_chromosomes=allowed_chromosomes,
        base_url=base_url,
    )
    print(result)





def handle_gff_annotate(args: argparse.Namespace) -> None:
    """Handle `modalysis gff annotate` CLI command."""
    base_url = f"http://localhost:{args.port}"
    result = gff_annotate(
        gff_path=args.gff_path,
        expression_paths=args.expression_paths,
        expression_labels=args.expression_labels,
        output_path=args.output_path,
        output_name=args.output_name,
        base_url=base_url,
    )
    print(result)