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A Python script that I want to use (called snakefood) is normally run from the commandline and takes commandline arguments, eg:

sfood /path/to/my/project

The parsing of the commandline arguments happens in a file called gendeps.py using optparse. However, I want to use the snakefood module from another script. Is there a way I can somehow mock the passing of commandline arguments to snakefood or a way of rewriting gendeps.py so that it doesn't depend on optparse anymore?

BioGeek
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1 Answers1

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You can always assign a new list to sys.argv:

import sys

sys.argv = ['programname', '-iq', '-q', directory]
gendeps.gendeps()

optparse uses sys.argv[1:] as input when no explicit arguments have been passed in.

Martijn Pieters
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  • This answer is helpful. Just a small improvement: `import os` `sys.argv = [os.path.basename(__file__),, '-iq', '-q', directory]` – mMontu Jul 03 '20 at 08:16