How to call module written with argparse in iPython notebook

I ended up using BioPython to extract the sequences and then editing Ilya Steanov’s implementation to remove the argparse methods.

import imp
seqs = []
lcsm = imp.load_source('lcsm', '/path/to/ukkonen.py')
for record in SeqIO.parse('/path/to/sequences.txt', 'fasta'):
    seqs.append(record)
lcsm.main(seqs)

For the algorithm, I had main() take one argument, his strings variable, but this sends the algorithm a list of special BioPython Sequence objects, which the re module doesn’t like. So I had to extract the sequence string

suffix_tree.append_string(s)

to

suffix_tree.append_string(str(s.seq))

which seems kind of brittle, but that’s all I’ve got for now.

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(argparse.Namespace):
  data = './data/penn'
  model = 'LSTM'
  emsize = 200
  nhid = 200

args=Args()

I face a similar problem in invoking argsparse, the string ‘-f’ was causing this problem. Just removing that from sys.srgv does the trick.

import sys
if __name__ == '__main__':
    if '-f' in sys.argv:
        sys.argv.remove('-f')
    main()

Clean sys.argv

import sys; sys.argv=['']; del sys

https://github.com/spyder-ide/spyder/issues/3883#issuecomment-269131039

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)

If you don’t want to change any of the arguments and working mechanisms from the original argparse function you have written or copied.

To let the program work then there is a simple solution that works most of the time.

You could just install jupyter-argparser using the below command:

pip install jupyter_argparser

The codes work without any changes thanks to the maintainer of the package.

Here is my code which works well and I won’t worry about the environment changed.

import sys
temp_argv = sys.argv

try:
    sys.argv = ['']
    print(sys.argv)
    args = argparse.parser_args()
finally:
    sys.argv = temp_argv
    print(sys.argv)

Suppose you have this small code in python:

import argparse

parser = argparse.ArgumentParser()
parser.add_argument("-v", "--verbose", help="increase output verbosity",
                    action="store_true")
parser.add_argument("-v_1", "--verbose_1", help="increase output verbosity",
                    action="store_true")
args = parser.parse_args()

To write this code in Jupyter notebook write this:

import argparse

args = argparse.Namespace(verbose=False, verbose_1=False)

Note: In python, you can pass arguments on runtime but in the Jupyter notebook that will not be the case so be careful with the data types of your arguments.

If arguments passed by the iPython environment can be ignored (do not conflict with the specified arguments), then the following works like a charm:

# REPLACE   args = parser.parse_args()   with:
args, unknown = parser.parse_known_args()

From: https://stackoverflow.com/a/12818237/11750716