Python argparse error

Question

This is my first time using python's argparse and I am not sure where am I doing wrong. Here is my code:

#!/usr/bin/env python

import argparse

parser = argparse.ArgumentParser(description='Example of argparse')

parser.add_argument('-i','--input', help='Input fasta file', required=True)
parser.add_argument('-o','--output', help='Output text file', required=True)
args = parser.parse_args()

genes = {} # empty list

with open(input, 'r') as fh_in:
        for line in fh_in:
                line = line.strip()
                if line[0] == ">":
                        gene_names = line[1:]
                        genes[gene_names] = ''
                else:
                        genes[gene_names]+=line


for (name,val) in genes.items():
        with open(output, "w") as fh_out:
                val = len(val)
                fh_out.write('%s %s' % (name,val))
                fh_out.write("\n")

And when i try to run it i get this error

python get_gene_length.py -i test_in.fa -o test_out.txt
Traceback (most recent call last):
  File "get_gene_length.py", line 13, in <module>
    with open(input, 'r') as fh_in:
TypeError: coercing to Unicode: need string or buffer, builtin_function_or_method found

Can anyone help me understand where should I make changes to the script to make it work?

wim · Accepted Answer · 2016-04-06 20:32:30Z

2

The arguments are parsed into a namespace object args. You'll need to use args.input instead of input, which is a name already referring to a built-in function.

Similarly for opening the output file later on.

answered Apr 6, 2016 at 20:32

wim

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1 Comment

upendra Over a year ago

It worked after changing the input to args.input and similarly for output. This is great help!

Perry · Accepted Answer · 2016-04-06 20:33:34Z

2

You never define the variable input anywhere, but then use it in your code. However, input is the name of a built in python function, resulting in this error instead of a NameError.

answered Apr 6, 2016 at 20:33

Perry

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