I know this is a very broad question but I'm learning about data science, I've been reading up on it for a few days and I can't find any info on how to manipulate a video game using python.
Can I use autopy and scikit-learn to make something similar to this?
Well, from what one can digest from source, this is a combination of neural network and genetic algorithm implementation. The author's approach is described in head of the source file:
There seem to be no problem in following this approach in python. You can get inspiration from the author's code or even use prepacked solutions like pyevolve for genetic algorithm implementation in python.