Python Forum

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

"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.

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.