sanitize_interproscan_tsv.py

#!/usr/bin/env python3

"""
Created by: Lee Bergstrand

Description: Makes newer InterProScan TSV file compatible with Pygenprop.

Requirements:  None

"""
import argparse
import csv
import os


def main(args):
    """
    Makes newer InterProScan TSV file compatible with Pygenprop.
    :param args: CLI Arguments
    """
    path = args.input
    path_filename = os.path.splitext(path)[0]
    new_path = os.path.join(path_filename + ".tsv2")

    with open(new_path, 'w') as new_tsv_file:
        with open(path, 'r') as tsv_file:
            reader = csv.reader(tsv_file, delimiter='\t')
            writer = csv.writer(new_tsv_file, delimiter='\t')
            for row in reader:
                if row[8] == '-':
                    row[8] = 1337
                new_row = ['' if value == '-' else value for value in row]
                writer.writerow(new_row)


if __name__ == '__main__':
    cli_title = """Makes newer InterProScan TSV file compatible with Pygenprop. Replaces '-' (indicating no value) 
    with no blank values. Blank values in the TSV e_value column with 1337."""

    parser = argparse.ArgumentParser(description=cli_title)
    parser.add_argument('-i', '--input', metavar='TSV', required=True,
                        help='The path to the InterProScan TSV to be sanitized.')

    cli_args = parser.parse_args()

    main(cli_args)