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