Source code for dae.genomic_resources.draw_score_histograms

import argparse
import os
import sys

from dae.gene_scores.gene_scores import (
    GeneScoresDb,
    build_gene_score_from_resource,
)
from dae.genomic_resources.cli import (
    _create_proto,
    _find_resource,
)
from dae.genomic_resources.genomic_scores import build_score_from_resource
from dae.genomic_resources.histogram import (
    NullHistogram,
    plot_histogram,
)
from dae.genomic_resources.repository import (
    GR_CONTENTS_FILE_NAME,
    ReadWriteRepositoryProtocol,
)
from dae.utils.fs_utils import find_directory_with_a_file
from dae.utils.verbosity_configuration import VerbosityConfiguration




def parse_cli_arguments() -> argparse.ArgumentParser:
    """Create CLI parser."""
    parser = argparse.ArgumentParser(
        description="Draw histograms for genomic scores.")

    VerbosityConfiguration.set_arguments(parser)

    parser.add_argument(
        "-R",
        "--repository",
        help="Optional URL to the genomic resources repository.",
    )
    parser.add_argument(
        "-r",
        "--resource",
        help="Optional URL to the resource.",
    )

    return parser





def main(
        argv: list[str] | None = None,
) -> None:
    """Liftover dae variants tool main function."""
    # pylint: disable=too-many-locals,too-many-statements
    if argv is None:
        argv = sys.argv[1:]

    parser = parse_cli_arguments()
    args = parser.parse_args(argv)

    VerbosityConfiguration.set(args)

    repo_path = find_directory_with_a_file(
        GR_CONTENTS_FILE_NAME,
        args.repository,
    )
    if repo_path is None:
        current_path = args.repository
        if current_path is None:
            current_path = os.getcwd()
        print("Can't find repository starting from: %s", current_path)
        sys.exit(1)

    repo_url = str(repo_path)
    print(f"working with repository: {repo_url}")

    proto = _create_proto(repo_url)

    if not isinstance(proto, ReadWriteRepositoryProtocol):
        raise TypeError(
            f"resource management works with RW protocols; "
            f"{proto.proto_id} ({proto.scheme}) is read only")

    res = _find_resource(proto, repo_url, resource=args.resource)
    if res is None:
        print("Resource not found...")
        sys.exit(1)

    assert res.config is not None
    if res.config.get("type") == "gene_score":
        gene_score = build_gene_score_from_resource(res)
        score_descs = GeneScoresDb.build_descs_from_score(gene_score)

        for score_desc in score_descs:
            image_filename = gene_score.get_histogram_image_filename(
                score_desc.score_id)
            plot_histogram(
                res,
                image_filename,
                score_desc.hist,
                score_desc.score_id,
                score_desc.small_values_desc,
                score_desc.large_values_desc,
            )
    else:
        genomic_score = build_score_from_resource(res)
        score_ids = genomic_score.get_all_scores()

        for score_id in score_ids:
            hist = genomic_score.get_score_histogram(score_id)
            if isinstance(hist, NullHistogram):
                continue
            image_filename = genomic_score.get_histogram_image_filename(
                score_id)
            score_def = genomic_score.score_definitions[score_id]
            small_values_desc = score_def.small_values_desc
            large_values_desc = score_def.large_values_desc
            plot_histogram(
                res,
                image_filename,
                hist,
                score_id,
                small_values_desc,
                large_values_desc,
            )