create_cross_species_motifs_rankings_db.py

#!/usr/bin/env python3

"""
Purpose :      Create cisTarget cross-species motif rankings databases.

Copyright (C): 2020-2021 - Gert Hulselmans
"""


import argparse
import glob
import os
import re
import sys
import time
from typing import List

from cistarget_db import CisTargetDatabase, DatabaseTypes

ct_rankings_db_motifs_vs_regions_or_genes_species_pattern = re.compile(
    r"""^(?P<db_prefix_minimal>.*?)(\.(?P<species>(?!(part[^.]+[0-9]+)|cross_?species)[^.]+))\.(?P<db_type>(?P<motifs_or_tracks_type>motifs)_vs_(?P<regions_or_genes_type>regions|genes)\.rankings\.feather)$"""
)


def create_cross_species_motifs_rankings_db(
    cross_species_db_prefix: str,
    ct_rankings_db_motifs_vs_regions_or_genes_species_filenames: List[str],
):

    cross_species_db_prefix = (
        cross_species_db_prefix
        if cross_species_db_prefix.endswith(".cross_species")
        else cross_species_db_prefix + ".cross_species"
    )

    start_creating_ct_cross_species_rankings_db_motifs_vs_regions_or_genes_time = (
        time.monotonic()
    )
    print(
        'Create cisTarget cross-species motifs rankings db from:\n  - "'
        + '"\n  - "'.join(ct_rankings_db_motifs_vs_regions_or_genes_species_filenames)
        + '"\n'
    )

    ct_cross_species_rankings_db_motifs_vs_regions_or_genes = CisTargetDatabase.create_cross_species_rankings_db(
        species_rankings_db_filenames=ct_rankings_db_motifs_vs_regions_or_genes_species_filenames
    )

    elapsed_creating_ct_cross_species_rankings_db_motifs_vs_regions_or_genes_time = (
        time.monotonic()
        - start_creating_ct_cross_species_rankings_db_motifs_vs_regions_or_genes_time
    )
    print(
        f"Creating cisTarget cross-species "
        f"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.column_kind} vs "
        f"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.row_kind} rankings db took: "
        f"{elapsed_creating_ct_cross_species_rankings_db_motifs_vs_regions_or_genes_time:.06f} seconds"
    )

    start_writing_ct_cross_species_rankings_db_motifs_vs_regions_or_genes_time = (
        time.monotonic()
    )
    ct_cross_species_rankings_db_motifs_vs_regions_or_genes_filename = ct_cross_species_rankings_db_motifs_vs_regions_or_genes.create_db_filename_from_db_prefix(
        db_prefix=cross_species_db_prefix, extension="feather"
    )
    print(
        f"Writing cisTarget cross-species "
        f"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.column_kind} vs "
        f"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.row_kind} rankings db: "
        f'"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes_filename}"'
    )

    ct_cross_species_rankings_db_motifs_vs_regions_or_genes.write_db(
        db_prefix=cross_species_db_prefix,
        version=2,
    )

    elapsed_writing_ct_cross_species_rankings_db_motifs_vs_regions_or_genes_time = (
        time.monotonic()
        - start_writing_ct_cross_species_rankings_db_motifs_vs_regions_or_genes_time
    )
    print(
        f"Writing cisTarget cross-species "
        f"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.column_kind} "
        f"vs {ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.row_kind} rankings db "
        f"took: {elapsed_writing_ct_cross_species_rankings_db_motifs_vs_regions_or_genes_time:.06f} seconds\n"
    )

    start_writing_ct_cross_species_rankings_db_regions_or_genes_vs_motifs_time = (
        time.monotonic()
    )
    ct_cross_species_rankings_db_regions_or_genes_vs_motifs_filename = DatabaseTypes.from_strings(
        scores_or_rankings="rankings",
        column_kind=ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.row_kind,
        row_kind=ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.column_kind,
    ).create_db_filename(
        db_prefix=cross_species_db_prefix, extension="feather"
    )
    print(
        f"Writing cisTarget cross-species "
        f"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.row_kind} vs "
        f"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.column_kind} rankings db: "
        f'"{ct_cross_species_rankings_db_regions_or_genes_vs_motifs_filename}"'
    )

    ct_cross_species_rankings_db_motifs_vs_regions_or_genes.transpose().write_db(
        db_prefix=cross_species_db_prefix,
        version=2,
    )

    elapsed_writing_ct_cross_species_rankings_db_regions_or_genes_vs_motifs_time = (
        time.monotonic()
        - start_writing_ct_cross_species_rankings_db_regions_or_genes_vs_motifs_time
    )
    print(
        f"Writing cisTarget cross-species "
        f"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.row_kind} vs "
        f"{ct_cross_species_rankings_db_motifs_vs_regions_or_genes.db_type.column_kind} rankings db "
        f"took: {elapsed_writing_ct_cross_species_rankings_db_regions_or_genes_vs_motifs_time:.06f} seconds\n"
    )


def main():
    parser = argparse.ArgumentParser(
        description="Create cisTarget cross-species motifs rankings databases."
    )

    parser.add_argument(
        "-i",
        "--input",
        dest="input",
        action="store",
        type=str,
        required=True,
        help="Input directory or database prefix with cisTarget motifs vs regions or genes rankings databases per "
        "species.",
    )

    parser.add_argument(
        "-o",
        "--output",
        dest="output_dir",
        action="store",
        type=str,
        required=True,
        help="Output directory to which the cisTarget cross-species motifs rankings database files will be written.",
    )

    args = parser.parse_args()

    # Construct glob string to find "*.*.motifs_vs_*.rankings.feather" cisTarget rankings database per species.
    ct_rankings_db_motifs_vs_regions_or_genes_species_glob_str = (
        os.path.join(args.input, "*.*.motifs_vs_*.rankings.feather")
        if os.path.isdir(args.input)
        else args.input + "*.*.motifs_vs_*.rankings.feather"
    )

    # Get all "*.*.motifs_vs_*.rankings.feather" cisTarget databases in the input directory or the ones that start with
    # the requested prefix.
    ct_rankings_db_motifs_vs_regions_or_genes_species_filenames = sorted(
        glob.glob(ct_rankings_db_motifs_vs_regions_or_genes_species_glob_str)
    )

    if len(ct_rankings_db_motifs_vs_regions_or_genes_species_filenames) == 0:
        print(
            f"Error: No cisTarget motifs vs regions or genes rankings databases per species found matching "
            f'glob: "{ct_rankings_db_motifs_vs_regions_or_genes_species_glob_str}".',
            file=sys.stderr,
        )
        sys.exit(1)

    ct_dbs_hierarchical_dict = dict()

    for (
        ct_rankings_db_motifs_vs_regions_or_genes_species_filename
    ) in ct_rankings_db_motifs_vs_regions_or_genes_species_filenames:
        # Parse cisTarget database filename, so databases made from the same regions/genes, but lifted over
        # to different species can be grouped together.
        match = ct_rankings_db_motifs_vs_regions_or_genes_species_pattern.match(
            ct_rankings_db_motifs_vs_regions_or_genes_species_filename
        )

        if match:
            db_prefix_minimal = match.group("db_prefix_minimal")
            db_type = match.group("db_type")
            species = match.group("species")

            ct_dbs_hierarchical_dict.setdefault(db_prefix_minimal, dict())
            ct_dbs_hierarchical_dict[db_prefix_minimal].setdefault(db_type, dict())
            ct_dbs_hierarchical_dict[db_prefix_minimal][db_type].setdefault(
                species, dict()
            )
            ct_dbs_hierarchical_dict[db_prefix_minimal][db_type][
                species
            ] = ct_rankings_db_motifs_vs_regions_or_genes_species_filename

    for db_prefix_minimal in ct_dbs_hierarchical_dict:
        for db_type in ct_dbs_hierarchical_dict[db_prefix_minimal]:
            # Get all cisTarget motifs vs regions or genes species rankings databases for the same regions/genes.
            ct_rankings_db_motifs_vs_regions_or_genes_species_filenames = [
                ct_dbs_hierarchical_dict[db_prefix_minimal][db_type][species]
                for species in sorted(
                    ct_dbs_hierarchical_dict[db_prefix_minimal][db_type]
                )
            ]

            create_cross_species_motifs_rankings_db(
                cross_species_db_prefix=db_prefix_minimal,
                ct_rankings_db_motifs_vs_regions_or_genes_species_filenames=ct_rankings_db_motifs_vs_regions_or_genes_species_filenames,
            )


if __name__ == "__main__":
    main()