4 ms·
Sure there are better alternatives, but the advantage of bash / shell scripting is that it’s very easy to glue a whole collection of tools together, and that ex
by stingraycharles 5y ago
Sure there are better alternatives, but the advantage of bash / shell scripting is that it’s very easy to glue a whole collection of tools together, and that expertise in this transfers well between domains.
They probably could have achieved the same by invoking things in Python, but it would have been slower and not achieved a lot, other than “not using shell scripts”.
And once you go down the path of optimizing this enough, you’ll end up reinventing shell scripts altogether.
- sanxiyn 5y agoWell, AlphaFold 2 generates MSA by invoking things in Python: https://github.com/deepmind/alphafold/blob/main/alphafold/data/tools/jackhmmer.py https://github.com/deepmind/alphafold/blob/main/alphafold/da.... So the article is actually mistaken on this point.