I have integrated a bash command into my Python code - how can I get this command to take an input from the shell?

Question

I have added a bash command to my Python script - this bash command is used to linearise an input file (i.e. take a file with many lines, and merge it into one line). It works when I manually write the name of the file for the command (in this example, the input file is called input.txt):

import subprocess

holder = subprocess.Popen('perl -ne "chomp;print;" input.txt', shell=True, stdout=subprocess.PIPE).stdout.read()

print(holder)

However, I would like this bash command to take the name of the file specified by the user in the command line, and linearise it.

I have already tried to achieve this using %s:

import subprocess
import sys
import os

path = sys.argv[1]
file = open(path, 'r')
inp = file.read()

holder = subprocess.Popen('perl -ne "chomp;print;" %s' % inp, shell=True, stdout=subprocess.PIPE).stdout.read()

print(holder)

However, when I try this, the shell freezes and shows no output, and the bash $ prompt does not show, there is no error message.

I would like to know if there is a valid way to add a user input in this case and would appreciate any help.

EDIT: just to clarify, here is what I type into my shell to run the program with the second example:

$ python3 program.py input.txt

Christian W. · Accepted Answer · 2019-08-12 09:11:32Z

2

Why not just directly feed the input path to your subprocess, like this? I'm slightly confused as to why you would like to use perl within python do this however..

import subprocess
import sys
import os

path = sys.argv[1]

holder = subprocess.Popen('perl -ne "chomp;print;" %s' % path, shell=True, stdout=subprocess.PIPE).stdout.read()

print(holder)

with this example input:

test.txt
i
i
i
i
i

the program will output:

python linearize.py test.txt
b'iiiii'

answered Aug 12, 2019 at 9:11

Christian W.

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1 Comment

agatha Over a year ago

Thank you very much. I realise that it's not good practice, but in this case I am pressed for time - as a beginner in Python it was taking me too long to work out how to linearise the type of file I'm inputting using Python.

Corentin Limier · Accepted Answer · 2019-08-12 09:25:55Z

2

import subprocess
import sys
import os

holder = subprocess.Popen('perl -ne "chomp;print;" {}'.format(sys.argv[1]), shell=True, stdout=subprocess.PIPE).stdout.read()

print(holder)

But why ? Why calling a perl script using python ? Python has all the tools you need to do the same using native, debuggable and crossplatform code on one process. It does not make sense and it is a bad practice.

import sys

with open(sys.argv[1]) as input_file:
    holder = ''.join(input_file.read().splitlines())

print(holder)

edited Aug 12, 2019 at 9:25

answered Aug 12, 2019 at 9:12

Corentin Limier

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3 Comments

agatha Over a year ago

Thank you for your help. I realise that it's not good practice, but in this case I am pressed for time - as a beginner in Python it was taking me too long to work out how to linearise the type of file I'm inputting using Python.

Corentin Limier Over a year ago

Btw, searching "remove carriage return + python" on SO gives you hundreds of solutions.

agatha Over a year ago

I have since realised that the perl script is not good for my purpose, as I am working with FASTA files and need to maintain separation of sequences. Your Python code works perfectly for what I described in this question though. However, I have posted a new question with a different command now.

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