Using python to call Emboss wordcount

Question

Hi guys I would like to run wordcount from Emboss in a bunch of fasta files. I tried this:

#!/usr/bin/env python
import sys
import subprocess



filenames = ['Downloads/Data/GCF_000016725.1_chr.fna']
for filename in filenames:
    name = filename.split('/')[2]
    print(filename)
    subprocess.call (['wordcount', 'Input sequence(s): ' + filename, 'Word size [4]: ' + sys.argv[1]])

But I got error messages:

Count and extract unique words in molecular sequence(s)
Error: Failed to open filename 'Input sequence(s): Downloads/Data/GCF_000016725.1_chr.fna'
Error: Unable to read sequence 'Input sequence(s): Downloads/Data/GCF_000016725.1_chr.fna'
Died: wordcount terminated: Bad value for '-sequence' and no prompt

But if a use shell with Downloads/Data/GCF_000016725.1_chr.fna it works fine!

Any tip would be helpful! I am using python, but I would have a method to compare my results!

Thank you by your time!

Paulo

Answer 1

You have to use command line options, not interactive prompts, like so:

subprocess.call(['wordcount', '-sequence', filename, '-wordsize', sys.argv[1]], '-outfile', filename + '.wordcount.txt')

Or, using the f-strings or formatted string literals:

subprocess.call(f'wordcount -sequence {filename} -wordsize {sys.argv[1]} -outfile {filename}.wordcount.txt')

Note that I had to add -outfile option to your system call, otherwise wordcount prompts for the output file. See wordcount manual.