How to call module written with argparse in iPython notebook

I am trying to pass BioPython sequences to Ilya Stepanov's implementation of Ukkonen's suffix tree algorithm in iPython's notebook environment. I am stumbling on the argparse component.

I have never had to deal directly with argparse before. How can I use this without rewriting main()?

By the by, this writeup of Ukkonen's algorithm is fantastic.

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

Using args = parser.parse_args(args=[]) would solve execution problem.

or you can declare it as class format.

class Args:
  data = './data/penn'
  model = 'LSTM'
  emsize = 200
  nhid = 200

args=Args()

I've had a similar problem before, but using optparse instead of argparse.

You don't need to change anything in the original script, just assign a new list to sys.argv like so:

if __name__ == "__main__":
    from Bio import SeqIO
    path = '/path/to/sequences.txt'
    sequences = [str(record.seq) for record in  SeqIO.parse(path, 'fasta')]
    sys.argv = ['-f'] + sequences
    main()

If all arguments have a default value, then adding this to the top of the notebook should be enough:

import sys
sys.argv = ['']

(otherwise, just add necessary arguments instead of the empty string)