a shell command is not writing in a file in python code

Question

While using the TreeTagger the following problem occured

import os
os.system("bin/tree-tagger lib/english-utf8.par inputfile outputfile")

The snippet above works in the command line. But when I try to execute it in a python code, nothing is written in the output file even though any error is given.

Possible duplicate of [Passing arguments into os.system](https://stackoverflow.com/questions/14892355/passing-arguments-into-os-system) — dtell, Jun 19 '18 at 15:09
don't use os.system, use `subprocess` with an arguments list. That'll be better already. — Jean-François Fabre, Jun 19 '18 at 15:31
I am not good at python programming. but I tried the below too. subprocess.call(["bin/tree-tagger lib/mongolian.par mon mon1 -token"], shell=True) — Ganchimeg, Jun 19 '18 at 15:38
don't do this, try `subprocess.check_call(["bin/tree-tagger","lib/mongolian.par mon","mon1","-token"], shell=False)` — Jean-François Fabre, Jun 19 '18 at 16:08
note that the command line in your question is different.... — Jean-François Fabre, Jun 19 '18 at 16:09
@Ganchimeg could you provide example files for every file you are using? We can then try to reproduce the behaviour you are observing. — dtell, Jun 20 '18 at 12:23

score 0 · Answer 1 · answered Jun 20 '18 at 15:31

This is the way I used cmd to include a command line within a programme I wrote a while ago in python 2.7. Obviously you will have to change for your type of data.

`import sys, os, subprocess
def velvet_assembly(fastqs,output):

    #cmd is a command line within the programme#
    cmd=['velveth', output, '59', '-fastq.gz', '-shortPaired',fastqs[0],fastqs[1]]
    my_file=subprocess.Popen(cmd)
    my_file.wait()
velvet_assembly(fastqs,output)`

In this link you can get some other examples. [https://www.cyberciti.biz/faq/python-run-external-command-and-get-output/][1]

Hope this is useful.

a shell command is not writing in a file in python code

1 Answers1