Source code for modalysis.cli.handlers.dmr

"""CLI handlers for DMR commands."""

import argparse
import logging

from modalysis.client.dmr import (
    dmr_annotate,
    dmr_common_genes,
    dmr_format,
    dmr_gene_counts,
)

logger = logging.getLogger(__name__)




def handle_dmr_format(args: argparse.Namespace) -> None:
    """Handle `modalysis dmr 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 = dmr_format(
        input_path=args.input_path,
        output_path=args.output_path,
        output_name=args.output_name,
        allowed_chromosomes=allowed_chromosomes,
        min_score=args.min_score,
        max_p_value=args.max_p_value,
        min_pct_a_samples=args.min_pct_a_samples,
        min_pct_b_samples=args.min_pct_b_samples,
        min_reads=args.min_reads,
        base_url=base_url,
    )
    print(result)





def handle_dmr_annotate(args: argparse.Namespace) -> None:
    """Handle `modalysis dmr annotate` CLI command."""
    base_url = f"http://localhost:{args.port}"
    result = dmr_annotate(
        dmr_path=args.dmr_path,
        gff_path=args.gff_path,
        output_path=args.output_path,
        output_name=args.output_name,
        base_url=base_url,
    )
    print(result)





def handle_dmr_gene_counts(args: argparse.Namespace) -> None:
    """Handle `modalysis dmr gene-counts` CLI command."""
    base_url = f"http://localhost:{args.port}"
    result = dmr_gene_counts(
        annotated_dmr_paths=args.annotated_dmr_paths,
        manifestations=args.manifestations,
        modifications=args.modifications,
        manifestation_labels=args.manifestation_labels,
        expression_labels=args.expression_labels,
        annotated_gff_path=args.annotated_gff_path,
        output_path=args.output_path,
        output_name=args.output_name,
        output_excel=args.output_excel,
        base_url=base_url,
    )
    print(result)





def handle_dmr_common_genes(args: argparse.Namespace) -> None:
    """Handle `modalysis dmr common-genes` CLI command."""
    base_url = f"http://localhost:{args.port}"
    result = dmr_common_genes(
        annotated_dmr_paths=args.annotated_dmr_paths,
        manifestations=args.manifestations,
        modifications=args.modifications,
        manifestation_labels=args.manifestation_labels,
        expression_labels=args.expression_labels,
        modification_a=args.modification_a,
        modification_b=args.modification_b,
        annotated_gff_path=args.annotated_gff_path,
        output_path=args.output_path,
        output_name=args.output_name,
        base_url=base_url,
    )
    print(result)