Formatting a command in python subprocess popen

Question

I am trying to format the following awk command

awk -v OFS=\"\\t\" \'{printf \"chr%s\\t%s\\t%s\\n\", $1, $2-1, $2}\' file1.txt > file2.txt

Answer 1

> is the shell redirection operator. To implement it in Python, use stdout parameter:

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

cmd = r"""awk -v OFS="\t" '{printf "chr%s\t%s\t%s\n", $1, $2-1, $2}'"""
with open('file2.txt', 'wb', 0) as output_file:
    subprocess.check_call(shlex.split(cmd) + ["file1.txt"], stdout=output_file)

To avoid starting a separate process, you could implement this particular awk command in pure Python.