Source code for aspring.step_06_stats

""" 
This scripts runs the step_06_getStats.R script 
"""
import os
import sys
import subprocess
import argparse

from aspring import __version__


def test_rscript_availability():
    try:
        cmd = ["Rscript", "--version"]
        subprocess.run(cmd,
                       check=True,
                       stdout=subprocess.DEVNULL,
                       stderr=subprocess.DEVNULL)
    except subprocess.CalledProcessError:
        raise Exception(
            "Rscript not found. Please install R and make sure Rscript is in your PATH."
        )


def run_r_script(gene, path_data):
    test_rscript_availability()
    aspring_path = os.path.dirname(os.path.abspath(__file__))
    renv_path = os.path.abspath(os.path.join(aspring_path, "R_script"))
    r_script_file = os.path.join(renv_path, "step_06_getStats.R")
    # Initialize the R environment
    subprocess.run(
        ["Rscript", "-e", "if (!require('renv')) install.packages('renv')"],
        check=True)
    subprocess.run(
        ["Rscript", "-e", "renv::restore(project='" + renv_path + "')"],
        check=True)

    # Run the R script
    try:
        subprocess.run(
            ["Rscript", r_script_file, "--gene", gene, "--path_data", path_data],
            check=True)
    except subprocess.CalledProcessError as err:
        # reraise the exception with a more informative message
        raise Exception("R script failed.") from err

def parse_args(args):
    parser = get_arg_parser()
    return parser.parse_args(args)

def get_arg_parser():
    parser = argparse.ArgumentParser(
        description="Generates statistics on the filtered duplicated regions.")
    parser.add_argument('--gene', required=True, help='Gene name')
    parser.add_argument('--path_data',
                        required=True,
                        help='Path to dir containing Thoraxe outputs')
    parser.add_argument('--version',
                        action='version',
                        version=f"aspring {__version__}")
    return parser


def run():
    args = parse_args(sys.argv[1:])
    gene = args.gene
    path_data = args.path_data
    run_r_script(gene, path_data)


if __name__ == '__main__':
    run()