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Add HA1 and NA mutation counts #201

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huddlej opened this issue Dec 19, 2024 · 0 comments
Open

Add HA1 and NA mutation counts #201

huddlej opened this issue Dec 19, 2024 · 0 comments
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enhancement New feature or request

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@huddlej
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huddlej commented Dec 19, 2024

Context

From @trvrb on Slack:

seasonal flu, we have epitope mutations for H3N2 and H1N1pdm, but strangely we don't have just HA1 mutations. (I no longer believe our split of epitope sites vs non-epitope sites is that accurate) We'll lacking any sorts for Vic and Yam. It would be nice to have HA1 mutation count for all 4. And NA mutation count as well for the NA tree.

Description

Define HA1 and NA distance maps for H1, H3, and B/Vic.

We already have a HA1 distance map for H3 and H1. We just need to create a similar JSON for B/Vic. For historical analyses, it would be useful to have one for B/Yam, too.

The NA mutation count would just require a simple Hamming distance map like this:

{
    "name": "NA",
    "default": 1,
    "map": {}
}

We could use that same map for all subtypes.

To include these distance calculations in the builds, we would need to add entries to the distance map configuration table and add colorings to the Auspice config JSONs for public and private builds.

@huddlej huddlej added the enhancement New feature or request label Dec 19, 2024
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