convert_motifs_or_tracks_vs_regions_or_genes_scores_to_rankings_cistarget_dbs.py

#!/usr/bin/env python3

"""
Purpose :      Convert cisTarget motifs or track vs regions or genes scores database to cisTarget rankings database.

Copyright (C): 2020-2022 - Gert Hulselmans
"""


import argparse
import random
import sys
import time

from cistarget_db import CisTargetDatabase, DatabaseTypes


def main():
    parser = argparse.ArgumentParser(
        description="Convert cisTarget motifs or tracks vs regions or genes scores database to cisTarget rankings"
        "database."
    )

    parser.add_argument(
        "-i",
        "--db",
        dest="ct_scores_db_motifs_or_tracks_vs_regions_or_genes_filename",
        action="store",
        type=str,
        required=True,
        help="cisTarget motifs or tracks vs regions or genes scores database filename. The cisTarget rankings database"
        "Feather file will be written to the same directory.",
    )

    parser.add_argument(
        "-s",
        "--seed",
        dest="seed",
        action="store",
        type=int,
        required=False,
        help="Random seed used for breaking ties when creating rankings for a range of tied scores. "
        "When setting this seed to a specific value and running this script with the same input, will result in "
        "the same cisTarget rankings databases as output.",
    )

    args = parser.parse_args()

    # Get cisTarget db type, db prefix and extension.
    (
        db_type,
        db_prefix,
        extension,
    ) = DatabaseTypes.create_database_type_and_db_prefix_and_extension_from_db_filename(
        db_filename=args.ct_scores_db_motifs_or_tracks_vs_regions_or_genes_filename
    )

    if db_type not in {
        DatabaseTypes.SCORES_DB_MOTIFS_VS_REGIONS,
        DatabaseTypes.SCORES_DB_MOTIFS_VS_GENES,
        DatabaseTypes.SCORES_DB_TRACKS_VS_REGIONS,
        DatabaseTypes.SCORES_DB_TRACKS_VS_GENES,
    }:
        print(
            f'Error: cisTarget database "{args.ct_scores_db_motifs_or_tracks_vs_regions_or_genes_filename}" is not a '
            "cisTarget motifs or tracks vs regions or genes scores database.",
            file=sys.stderr,
        )
        sys.exit(1)

    def write_db(ct_db: CisTargetDatabase, db_prefix: str):
        """
        Write cisTarget database to a Feather file and print database location and elapsed time.

        :param ct_db: cisTarget database object.
        :param db_prefix: Feather database file prefix.
        :return:
        """
        db_filename = ct_db.create_db_filename_from_db_prefix(
            db_prefix=db_prefix, extension="feather"
        )

        print(
            f"Writing cisTarget {ct_db.db_type.row_kind} vs {ct_db.db_type.column_kind} "
            f'{ct_db.db_type.scores_or_rankings} db: "{db_filename}"'
        )

        start_time = time.monotonic()
        ct_db.write_db(
            db_prefix=db_prefix,
            version=2,
        )
        elapsed_time = time.monotonic() - start_time

        print(
            f"Writing cisTarget {ct_db.db_type.row_kind} vs {ct_db.db_type.column_kind} "
            f"{ct_db.db_type.scores_or_rankings} db took: {elapsed_time:.06f} seconds\n"
        )

    # Create cisTarget rankings database (motifs or tracks vs regions or genes) from cisTarget scores database filename
    # (motifs or tracks vs regions or genes).
    start_reading_ct_scores_db_motifs_or_tracks_vs_regions_or_genes_db_time = (
        time.monotonic()
    )
    print(
        f"\nReading cisTarget {db_type.column_kind} vs {db_type.row_kind} "
        f'scores db: "{args.ct_scores_db_motifs_or_tracks_vs_regions_or_genes_filename}"'
    )

    ct_scores_db_motifs_or_tracks_vs_regions_or_genes = CisTargetDatabase.read_db(
        db_filename_or_dbs_filenames=args.ct_scores_db_motifs_or_tracks_vs_regions_or_genes_filename
    )

    elapsed_reading_ct_scores_db_motifs_or_tracks_vs_regions_or_genes_db_time = (
        time.monotonic()
        - start_reading_ct_scores_db_motifs_or_tracks_vs_regions_or_genes_db_time
    )
    print(
        f"Reading cisTarget {db_type.column_kind} vs {db_type.row_kind} scores db took: "
        f"{elapsed_reading_ct_scores_db_motifs_or_tracks_vs_regions_or_genes_db_time:.06f} seconds\n"
    )

    # Set random seed to provided input value or a random integer.
    seed = args.seed if args.seed else random.randint(0, 2**64)

    # Create cisTarget rankings database (motifs or tracks vs regions or genes) from cisTarget scores database filename
    # (motifs or tracks vs regions or genes).
    start_creating_rankings_ct_rankings_db_motifs_or_tracks_vs_regions_or_genes_db_time = (
        time.monotonic()
    )
    print(
        f'Create rankings from "{args.ct_scores_db_motifs_or_tracks_vs_regions_or_genes_filename}" with random seed '
        f"set to {seed}."
    )

    ct_rankings_db_motifs_or_tracks_vs_regions_or_genes = ct_scores_db_motifs_or_tracks_vs_regions_or_genes.convert_scores_db_to_rankings_db(
        seed=seed
    )

    elapsed_creating_rankings_ct_rankings_db_motifs_or_tracks_vs_regions_or_genes_db_time = (
        time.monotonic()
        - start_creating_rankings_ct_rankings_db_motifs_or_tracks_vs_regions_or_genes_db_time
    )
    print(
        f"Creating cisTarget rankings db from cisTarget scores db took: "
        f"{elapsed_creating_rankings_ct_rankings_db_motifs_or_tracks_vs_regions_or_genes_db_time:.06f} seconds\n"
    )

    # Reclaim memory occupied by motifs or tracks vs regions or genes cisTarget scores database.
    del ct_scores_db_motifs_or_tracks_vs_regions_or_genes

    # Do not write cisTarget rankings database (motifs or tracks vs regions or genes) to
    # Feather file as it can take a very long time to write it (1.5 hours for 1 milion
    # regions) as the rankings database numpy array is in "C" order and writing a Feather
    # database requires travering the numpy array in column order.
    # write_db(ct_db=ct_rankings_db_motifs_or_tracks_vs_regions_or_genes, db_prefix=db_prefix)

    # Create cisTarget rankings database (regions or genes vs motifs or tracks) from (motifs or tracks vs regions or
    # genes) version.
    print(
        f"Convert {db_type.column_kind} vs {db_type.row_kind} cisTarget rankings db to {db_type.row_kind} vs "
        f"{db_type.column_kind} cisTarget rankings db."
    )
    ct_rankings_db_regions_or_genes_vs_motifs_or_tracks = (
        ct_rankings_db_motifs_or_tracks_vs_regions_or_genes.transpose()
    )

    # Write cisTarget rankings database (regions or genes vs motifs or tracks) to Feather file.
    write_db(
        ct_db=ct_rankings_db_regions_or_genes_vs_motifs_or_tracks, db_prefix=db_prefix
    )


if __name__ == "__main__":
    main()