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biolink / ontobio

python library for working with ontologies and ontology associations
https://ontobio.readthedocs.io/en/latest/
BSD 3-Clause "New" or "Revised" License
119 stars 30 forks source link

bug fixes for writing gaf 2.2 #500

Closed dougli1sqrd closed 3 years ago

dougli1sqrd commented 3 years ago

For https://github.com/biolink/ontobio/issues/499

kltm commented 3 years ago

@dougli1sqrd I think everything here makes sense to me--merge when you're ready.

In general, I'd go ahead and error out on bad command input (e.g. GAF 3.1) rather than falling back to a sensible default. As this is often pipeline software, rather than interactive, it's best not to let things that could be seen as "data loss" leak in for QC later on to discover (or not!).

dougli1sqrd commented 3 years ago

That makes sense. This command and tool isn't used anywhere in the pipeline, and I don't think it ever will be. This is more of a human run tool these days.