IMGT update

[acrinklaw]

Adds a massive amount of data from the IMGT - all alleles are pulled into chain, chain-sequence, genetic-locus, and molecule.tsv. Molecule.tsv only has HLA-A,B,C,DQ,DR,DP per Randi's suggestion. Updates on the current IMGT release can be done by just calling python check_missing_alleles.py but output sheets need to be sorted.

I ran the validation and built locally to make sure it's okay and I didn't run into any issues. I also tried to adhere to some style guidelines I saw in knocean documentation such as using Black / f string syntax. Let me know if there are any other improvements or changes to make

[acrinklaw]

It looks like I need to update the index since things were added since I made the branch and then readd the new terms - I'll do this and rebuild + commit

[beckyjackson]

In the python script, I think the paths to files should be passed as command line args. You could just pass the path to the ontology/ directory and path to index.tsv.

Additionally, any time you're writing to one of the TSVs it would probably be better to use CSV writer instead of joining with \t.

I left comments in-line for most of them, but I stopped around line 300 since it was all just the same thing :)

Also, can we add this task to the Makefile? Maybe as make update-alleles.

[jamesaoverton]

I want to make some decisions about #37 before merging this. If we decide to move large mro.owl etc. out of version control, then I'll want a new branch (or just a squash commit?) that does not include the large files in our git history forever.

[beckyjackson]

I think squashing would still keep it in the git history (I might be wrong though?), but there are other ways to remove files: https://docs.github.com/en/github/managing-large-files/removing-files-from-a-repositorys-history

[jamesaoverton]

If we remove a large file from the branch, then squash merge to master, I think it will not appear in the history. I think we should end up with one commit that jumps over the large files that we don't want.

But I'm certain that if we create a clean branch to merge, and delete the dev branch with the large files without merging it, then the history will not include the large files.

[beckyjackson]

I created a clean PR in #39 to get rid of the "big" MRO.

[jamesaoverton]

Closing in favour of #39.