How to call module written with argparse in iPython notebook

An alternative to use argparse in Ipython notebooks is passing a string to:

args = parser.parse_args()
(line 303 from the git repo you referenced.)

Would be something like:

parser = argparse.ArgumentParser(
        description='Searching longest common substring. '
                    'Uses Ukkonen\'s suffix tree algorithm and generalized suffix tree. '
                    'Written by Ilya Stepanov (c) 2013')

parser.add_argument(
        'strings',
        metavar="STRING",
        nargs="*",
        help='String for searching',
    )

parser.add_argument(
        '-f',
        '--file',
        help='Path for input file. First line should contain number of lines to search in'
    )

and

args = parser.parse_args("AAA --file /path/to/sequences.txt".split())

Edit: It works