BLRunner.py

#!/usr/bin/env python
# coding: utf-8

import argparse
import time

import yaml

import BLRun as br

yaml.warnings({"YAMLLoadWarning": False})


def get_parser() -> argparse.ArgumentParser:
    """
    :return: an argparse ArgumentParser object for parsing command
        line parameters
    """
    parser = argparse.ArgumentParser(description="Run pathway reconstruction pipeline.")

    parser.add_argument("--config", default="config.yaml", help="Path to config file")

    return parser


def parse_arguments():
    """
    Initialize a parser and use it to parse the command line arguments
    :return: parsed dictionary of command line arguments
    """
    parser = get_parser()
    opts = parser.parse_args()

    return opts


def main():
    opts = parse_arguments()
    config_file = opts.config

    with open(config_file, "r") as conf:
        evaluation = br.ConfigParser.parse(conf)
    # print(evaluation.__dict__)
    start_time = time.process_time()
    print("Evaluation started")

    for idx in range(len(evaluation.runners)):
        evaluation.runners[idx].generateInputs()

    for idx in range(len(evaluation.runners)):
        evaluation.runners[idx].run()

    for idx in range(len(evaluation.runners)):
        evaluation.runners[idx].parseOutput()

    print("Evaluation complete")
    end_time = time.process_time()
    print(f"Execution of algorithms completed in {end_time-start_time:0.2f} seconds")


if __name__ == "__main__":
    main()