I am working on a module for

goatools find_enrichment

. It requires several files for testing: a gene ontology (

.obo

), an annotation (

.gaf

or another supported format), and two lists of genes (simple text files). As far as I see, none of these files are available in the test-datasets repo. I have some tiny mock data that works with the tool. Can someone better versed in test data direct me as to where I should put the files? Especially the lists, since they follow no standard format.

Is this what you are looking for? You have to create a branch and add your files to that. (That's my understanding, I've never don that, though.) I don't think the format matters per-se, it just needs to work with your tool(s).

I know the repo and the

modules

branch, but it has been problematic for a long time (and there have been many discussions about it), and I almost never know where to insert new data when it's needed. I ended up putting the data in a location that seemed fine.

Looking at the branch names, my best guess is that people make something up that is vaguely descriptive. The beauty of GitHub is that if someone doesn't like it, they can raise an issue or submit a pull request ... The problem of course is that with hundreds of branches it becomes hard to see what is already there and could be reused. Maybe there should be a "directory" in the

master

branch, but that would only be as useful as the contributors are diligent in keeping it up-to-date. Once you submit the module for general review, some people should ideally look at the tests as well.