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
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()