How to launch a program through python script - Mac OS Mojave

[Aurimas]

Dear Python forum members,

I am trying to write and launch a python script through terminal at Mac OS Mojave, however I am getting this error:

Error:
$ python bandom_voronota_paleisti.py 
> 3dvo.pdb1
sh: input_file: No such file or directory

The 3dvo.pdb1 file is in the exact location where I run the program from but it cannot be loaded through os.system, so I am puzzled

The code I have is this:

import sys, os

input_file_v2 = raw_input('> ')
input_file_v1 = open(input_file_v2, 'r+')
input_file = input_file_v1.read()
os.system("voronota get-balls-from-atoms-file --annotated < input_file") # doesn't work with input_file

Shouldn't it be possible to run my external program (voronota) that is run through terminal simply with raw_input? I have tried it but received the same error when not setting the input file to be readable. However, after setting it I still get this error. What could be the problem?

Thank you very much fo your assistance.

Sincerely,
Aurimas

[micseydel]

"input_file" is embedded as a string, it's not used as a variable. You need to do string formatting like so:

"voronota get-balls-from-atoms-file --annotated < {}".format(input_file)

Note that code like this is subject to security issues if anyone can specify the filename. Not likely an issue but hard to not at least bring up here.

[kritesh]

If you’re not familiar with the language, you can recognize scripts written in Python by their distinctive “.py” file extension. Python scripts can be executed in a couple different ways, depending on what tools you have at your disposal. Hope above information will help you.