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.
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()
print(args) it shows Args().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
args = parser.parse_args(['--file', '/path/to/sequences.txt']), i.e. you need to pass an array of strings where each element is an argument that would normally be separated by a space in the command line.
shlex.split: args = parser.parse_args(shlex.split("AAA --file /path/to/sequences.txt"))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)
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()
Clean sys.argv
import sys; sys.argv=['']; del sys
https://github.com/spyder-ide/spyder/issues/3883#issuecomment-269131039
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.
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()
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()
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.
