#!/usr/bin/env python3

"""
Bin executable fro command line usage

"""

import sys
import argparse
import logging

# Module import
from barseq.main import main


__author__ = "Emanuel Burgos"
__email__ = "eburgos@wisc.edu"

# Get logger
logger = logging.getLogger("barseq")


def parse_args(args):
    if not args:
        args = ["-h"]
    # Parse arguments
    parser = argparse.ArgumentParser('Python software for analyzing barseq data.')

    parser.add_argument("-i", "--input", help="Directory where fastq/fastq.gz files are located.")

    parser.add_argument("-b", "--barcodes", help="CSV file with barcodes for genes")

    parser.add_argument("-e", "--experiment", help="Name for experiment")

    # Process arguments given
    args = parser.parse_args(args)
    return args


if __name__ == '__main__':
    main(parse_args(sys.argv[1:]))
