main.py

import os
from config import Config, config_parser
from parsnp_alignment import run_parsnp
from alignments_filter import run_filter
from utils import (
    delete_files,
    get_today_datetime,
    create_dir,
)
import logging
import time
import sequence_finder
from report import create_general_report


def config_logging(log_dir: str):
    """
    Configures logging settings and sets up log file.

    Keyword arguments:
        log_dir (str): The directory path where the log file will be saved.

    Returns:
        None
    """
    output_filename_prefix = "LOG"
    log_file_name = f"{output_filename_prefix}_{time.strftime('%y_%m_%d_%H_%M')}.log"
    log_file_name_path = os.path.join(log_dir, log_file_name)
    logging.basicConfig(
        level=logging.INFO,
        filename=log_file_name_path,
        filemode="w",
        format="%(asctime)s %(levelname)s %(filename)s %(funcName)s(%(lineno)d) %(message)s",
    )
    logging.info("Logs have been setup!")


def setup_run():
    """
    This routine setup the config file based on the input parameters
    and the log file.'''

    Returns:
        Config: The configuration object containing the setup parameters.
    """
    config_args = None
    parser_args, _ = config_parser.parse_known_args()

    # Load input parameters
    config_args = Config(**vars(parser_args))

    # Verify output paths exit; otherwise create them.
    for path in [
        config_args.temp_path,
        config_args.output_path,
        config_args.output_parsnp_path,
        config_args.multifasta_path,
        config_args.in_process_path,
    ]:
        os.makedirs(path, exist_ok=True)

    # Create results folder
    dir_name = get_today_datetime()
    results_path = create_dir(config_args.output_path, dir_name)
    config_args.results_path = results_path
    # Write the config file to the results folder
    config_args.to_file()

    # Setup the logs
    config_logging(log_dir=results_path)

    return config_args


def main():
    """
    Main function that executes the alignment process.

    Returns:
        None
    """
    start = time.time()

    # Setup all the running parameters
    config_args = setup_run()
    config_args.stats.start_time = start

    if config_args == None:
        return

    # Log input parameters and config
    config_args._log()

    # Run parsnp
    success = True
    if config_args.xmfa_file_path == "" and config_args.filtered_xmfa_path == "":
        success = run_parsnp(config_args=config_args, reference_genome=None)

    # If success, filter alignments
    if success and config_args.filtered_xmfa_path == "":
        success = run_filter(config_args=config_args)

    if success:
        alignment_genomes = sequence_finder.get_unique_seq_from_alignments(
            config_args=config_args
        )
        end = time.time()
        mins = (end - start) / 60
        config_args.stats.end_time = end
        config_args.stats.total_runtime = mins
        create_general_report(
            config_args=config_args, unique_seq_candidates=alignment_genomes, mins=mins
        )

    if config_args.copied_ingroup_folder:
        delete_files(config_args.ingroup_path)
        os.rmdir(config_args.ingroup_path)

    if config_args.copied_outgroup_folder:
        delete_files(config_args.outgroup_path)
        os.rmdir(config_args.outgroup_path)

    logging.info(
        "Deleting temporal files -------------------------------------\n")
    delete_files(config_args.multifasta_path)
    delete_files(config_args.in_process_path)

    end = time.time()
    mins = (end - start) / 60

    logging.info("\n\n Total Runtime mins {}".format(mins))


if __name__ == "__main__":
    main()