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hodcroftlab / covariants

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
https://covariants.org/
GNU Affero General Public License v3.0
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Update clusters.py #260

Closed youngpe69 closed 2 years ago

youngpe69 commented 2 years ago

Not sure what threshold is being used for the mutations in the mutation table but am proposing to add Orb9b into the 21L.Omicron section based off populations from cov-spectrum for Denmark based of: Orf9b P10S (98.71), E27-(98.09), E28-(98.09), A29-(98.09). Hope that is okay and makes sense!

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emmahodcroft commented 2 years ago

Hi @youngpe69 - I'm sorry for the slow reply on this - I'm grant writing so CoVariants things are going more slowly than usual.

However, I checked this out and I agree, it looks to me like the ORF9b mutations in 21K are also in 21L. I'd be happy to approve this (well, with the small caveat that they should be 9b instead of 9a as is currently in the PR - but easily fixed!) - is there a reason you closed it?

emmahodcroft commented 2 years ago

Hi @youngpe69 - I'm going to make this fix in clusters.py, but I'd be very happy to credit you for spotting it, if you let me know a Twitter handle!

youngpe69 commented 2 years ago

Hi @emmahodcroft, apologies, just spotted this. Pulled the change because of 9a and also spotted the use of scripts to produce .json. Forced me to pull the codebase down and build locally etc which is a good thing! Will continue to have a think about gene selection on the mutation comparison page. Probably quite a substantial change there - I'll keep to the current UX design principles and current code design patterns.