Linux Command for Perl in Python

Question

I am trying to this Linux command for Perl (v5.10.1) in Python (v2.6)

perl tilt.pl *.pdb > final.txt

What do I do so that I can apply the Perl script to every PDB file, examples would be best?

my current script is this:

import shlex, subprocess
arg_str = "perl tilt.pl frames > final.txt"
arg = shlex.split(arg_str)

print(arg)

import os
framespdb = os.listdir("prac_frames")

for frames in framespdb:
        subprocess.Popen(arg, stdout=True)

furas · Accepted Answer · 2014-07-22 02:26:38Z

3

You can use shell=True

BTW: I think you try to put variable frames in place of text frames in command so I use %s and line % frames to do this.

import os
import subprocess

line = "perl tilt.pl %s > final.txt"

framespdb = os.listdir("prac_frames")

for frames in framespdb:
    cmd = line % frames
    print(cmd)
    subprocess.Popen(cmd, shell=True)

EDIT: if you need results in different files you can use again %s to add unique filename to command - for example:

import os
import subprocess

line = "perl tilt.pl %s > final-%s.txt" # second `%s`

framespdb = os.listdir("prac_frames")

for frames in framespdb:
    cmd = line % (frames, frames) # second `frames`
    print(cmd)
    subprocess.Popen(cmd, shell=True)

EDIT: normally in shell you can send result on screen or redirect it to file > file.txt. To get text on screen and save it in file you need shell command tee and python command subprocess.check_output():

import os
import subprocess

line = "perl tilt.pl %s | tee final-%s.txt"

framespdb = os.listdir("prac_frames")


for frames in framespdb:
    cmd = line % (frames, frames)
    print(cmd)
    output = subprocess.check_output(cmd, shell=True)
    print 'output:', output

edited Jul 22, 2014 at 2:26

answered Jul 22, 2014 at 1:47

furas

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3 Comments

Chemist not a Programmer Over a year ago

That worked very well. How would I get the out put in a text file from this? I keep getting "Stop! File 'content from prac_frames' not not found!"

furas Over a year ago

output goes to final.txt and overwrite previous result - you can use >> to get all results in final.txt. Or you can use another %s in line to save to different files. See new example in answer.

furas Over a year ago

if you need result from perl script in python script then perl script has to print it on screen (it's call output in doumentation) but normal redirection > send result to file - not on screen. You need shell command tee to send perl script result on screen and into file. See new example.

Andrew Johnson · Accepted Answer · 2014-07-22 01:43:07Z

1

You can call a subprocess like from the shell if you override the shell parameter:

subprocess.call(arg_str, shell=True)

answered Jul 22, 2014 at 1:43

Andrew Johnson

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