#!/opt/conda/conda-bld/pyscenic_1730217136194/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/bin/python

import argparse
import sys
import time
from functools import partial
from multiprocessing import Pool, cpu_count
from pathlib import PurePath

import loompy as lp
import pandas as pd
import tqdm
from arboreto.algo import _prepare_input, genie3, grnboost2
from arboreto.core import (
    EARLY_STOP_WINDOW_LENGTH,
    RF_KWARGS,
    SGBM_KWARGS,
    infer_partial_network,
    target_gene_indices,
    to_tf_matrix,
)
from arboreto.utils import load_tf_names

from pyscenic.cli.utils import load_exp_matrix, suffixes_to_separator


def create_argument_parser():
    parser = argparse.ArgumentParser(
        description="Run Arboreto using a multiprocessing pool"
    )

    parser.add_argument(
        "expression_mtx_fname",
        type=str,
        help="The name of the file that contains the expression matrix for the single cell experiment."
        " Two file formats are supported: csv (rows=cells x columns=genes) or loom (rows=genes x columns=cells).",
    )
    parser.add_argument(
        "tfs_fname",
        type=str,
        help="The name of the file that contains the list of transcription factors (TXT; one TF per line).",
    )
    parser.add_argument(
        "-m",
        "--method",
        choices=["genie3", "grnboost2"],
        default="grnboost2",
        help="The algorithm for gene regulatory network reconstruction (default: grnboost2).",
    )
    parser.add_argument(
        "-o",
        "--output",
        type=str,
        default=sys.stdout,
        help="Output file/stream, i.e. a table of TF-target genes (TSV).",
    )
    parser.add_argument(
        "--num_workers",
        type=int,
        default=cpu_count(),
        help="The number of workers to use. (default: {}).".format(cpu_count()),
    )
    parser.add_argument(
        "--seed",
        type=int,
        required=False,
        default=None,
        help="Seed value for regressor random state initialization (optional)",
    )

    parser.add_argument(
        "--cell_id_attribute",
        type=str,
        default="CellID",
        help="The name of the column attribute that specifies the identifiers of the cells in the loom file.",
    )
    parser.add_argument(
        "--gene_attribute",
        type=str,
        default="Gene",
        help="The name of the row attribute that specifies the gene symbols in the loom file.",
    )
    parser.add_argument(
        "--sparse",
        action="store_const",
        const=True,
        default=False,
        help="If set, load the expression data as a sparse (CSC) matrix.",
    )
    parser.add_argument(
        "-t",
        "--transpose",
        action="store_const",
        const="yes",
        help="Transpose the expression matrix (rows=genes x columns=cells).",
    )

    return parser


def run_infer_partial_network(
    target_gene_index,
    gene_names,
    ex_matrix,
    tf_matrix,
    tf_matrix_gene_names,
    method_params,
    seed,
):
    target_gene_name = gene_names[target_gene_index]
    target_gene_expression = ex_matrix[:, target_gene_index]

    n = infer_partial_network(
        regressor_type=method_params[0],
        regressor_kwargs=method_params[1],
        tf_matrix=tf_matrix,
        tf_matrix_gene_names=tf_matrix_gene_names,
        target_gene_name=target_gene_name,
        target_gene_expression=target_gene_expression,
        include_meta=False,
        early_stop_window_length=EARLY_STOP_WINDOW_LENGTH,
        seed=seed,
    )
    return n


def main():
    parser = create_argument_parser()
    args = parser.parse_args()

    if args.method == "grnboost2":
        method_params = ["GBM", SGBM_KWARGS]  # regressor_type  # regressor_kwargs
    elif args.method == "genie3":
        method_params = ["RF", RF_KWARGS]  # regressor_type  # regressor_kwargs

    start_time = time.time()
    ex_matrix = load_exp_matrix(
        args.expression_mtx_fname,
        (args.transpose == "yes"),
        args.sparse,
        args.cell_id_attribute,
        args.gene_attribute,
    )

    if args.sparse:
        gene_names = ex_matrix[1]
        ex_matrix = ex_matrix[0]
    else:
        gene_names = ex_matrix.columns

    end_time = time.time()
    print(
        f"Loaded expression matrix of {ex_matrix.shape[0]} cells and {ex_matrix.shape[1]} genes in {end_time - start_time} seconds...",
        file=sys.stdout,
    )

    tf_names = load_tf_names(args.tfs_fname)
    print(f"Loaded {len(tf_names)} TFs...", file=sys.stdout)

    ex_matrix, gene_names, tf_names = _prepare_input(ex_matrix, gene_names, tf_names)
    tf_matrix, tf_matrix_gene_names = to_tf_matrix(ex_matrix, gene_names, tf_names)

    print(
        f"starting {args.method} using {args.num_workers} processes...", file=sys.stdout
    )
    start_time = time.time()

    with Pool(args.num_workers) as p:
        adjs = list(
            tqdm.tqdm(
                p.imap(
                    partial(
                        run_infer_partial_network,
                        gene_names=gene_names,
                        ex_matrix=ex_matrix,
                        tf_matrix=tf_matrix,
                        tf_matrix_gene_names=tf_matrix_gene_names,
                        method_params=method_params,
                        seed=args.seed,
                    ),
                    target_gene_indices(gene_names, target_genes="all"),
                    chunksize=1,
                ),
                total=len(gene_names),
            )
        )

    adj = pd.concat(adjs).sort_values(by="importance", ascending=False)

    end_time = time.time()
    print(f"Done in {end_time - start_time} seconds.", file=sys.stdout)

    extension = PurePath(args.output).suffixes
    adj.to_csv(args.output, index=False, sep=suffixes_to_separator(extension))


if __name__ == "__main__":
    main()
