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.
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()
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
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.
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