feat(collection-seeder): add influenza resistance mutation collections#1316
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feat(collection-seeder): add influenza resistance mutation collections#1316fhennig wants to merge 4 commits into
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Adds four new Source classes (h1n1pdm, h3n2, h5n1, victoria) that fetch antiviral resistance mutation data from the BU-ISCIII flu_resistance repo and produce one Collection per antiviral per organism. NA inhibitors (Oseltamivir, Zanamivir, Peramivir, Laninamivir) are sourced from NA-inhibitors.json with NI/RI/HRI classification. Baloxavir is sourced from PA-inhibitors.json with fold-change values. NI-only and unknown (?, ?e) entries are excluded. Open questions about strain mapping, fold-change thresholds, LAPIS gene name conventions, and additional data files are documented in QUESTIONS.md. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Baloxavir variants now named by mutation (e.g. 'PA:I38T') with fold-change surfaced in the new variant description field - Add description field to Variant TypedDict (NotRequired[str]) - Remove QUESTIONS.md (all questions resolved) Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Some entries in NA-inhibitors.json have leading spaces (e.g. " S227N"), which produced invalid strings like "NA: S227N" in aminoAcidMutations. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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resolves #1272
Summary
There are still some TODOs left, but I need input from @DrYak for this.
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