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SPDI normalization with refseq files #76

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SPDI normalization with refseq files #76

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Commits on May 16, 2024

  1. Add SPDI normalization with refseq files

    @mihaitodor
    mihaitodor committed May 16, 2024
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  2. WIP

    @mihaitodor
    mihaitodor committed May 16, 2024
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  3. Test SPDI 3 bit packing RefSeq scheme

    @mihaitodor
    mihaitodor committed May 16, 2024
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  4. Disable some hgvs validations and rename some variables

    @mihaitodor
    mihaitodor committed May 16, 2024
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  5. Fix bit mask bug

    @mihaitodor
    mihaitodor committed May 16, 2024
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  6. Add historical RNA sequences

    @mihaitodor
    mihaitodor committed May 16, 2024
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  7. Set the HGVS_SEQREPO_URL env var for the hgvs library

    @mihaitodor
    mihaitodor committed May 16, 2024
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  8. Disable the HGVS library LRU cache to avoid blowing up memory

    @mihaitodor
    mihaitodor committed May 16, 2024
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  9. Add Normalize Variant utility

    @mihaitodor
    mihaitodor committed May 16, 2024
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  10. Output the projected HGVS variants via Normalize Variant

    @mihaitodor
    mihaitodor committed May 16, 2024
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  11. Update to the latest version of UTA

    @mihaitodor
    mihaitodor committed May 16, 2024
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  12. Re-enable variant validation

    @mihaitodor
    mihaitodor committed May 16, 2024
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  13. Fix CI/CD pipeline

    @mihaitodor
    mihaitodor committed May 16, 2024
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  14. Emit a 422 status when unable to normalize a variant

    @mihaitodor
    mihaitodor committed May 16, 2024
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  15. Use Heroku Prod UTA database

    @mihaitodor
    mihaitodor committed May 16, 2024
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  16. Add manual deployment instructions

    @mihaitodor
    mihaitodor committed May 16, 2024
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  17. Use Biocommons bioutils package for SPDI normalization

    @mihaitodor
    mihaitodor committed May 16, 2024
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  18. Emit a 404 status when the seqfetcher endpoint fails

    @mihaitodor
    mihaitodor committed May 16, 2024
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  19. Fix bug in get_variant and fix tests 

    Need to run the Flask server in a background thread so the
seqfetcher endpoint is available for the hgvs library to call.
Details here: https://stackoverflow.com/questions/77676757/run-a-full-flask-server-under-pytest-to-handle-http-requests-on-a-given-port

Also need to pick the relevat transcript in `process_NC_HGVS()` in
such a way that we select the one with the most up to date version
so we don't end up unable to find the RefSeq data because it looks
like we don't have all the RNA transcripts that UTA knows about.
    @mihaitodor
    mihaitodor committed May 16, 2024
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  20. Don't trim alleles when ref == alt for SPDI normalization

    @mihaitodor
    mihaitodor committed May 16, 2024
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  21. Disable HGVS strict bounds checks 

    This is a workaround for some liftover failures: biocommons/hgvs#717
    @mihaitodor
    mihaitodor committed May 16, 2024
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  22. Fix broken test which now works again as expected

    @mihaitodor
    mihaitodor committed May 16, 2024
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  23. Re-enable test

    @mihaitodor
    mihaitodor committed May 16, 2024
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  24. Add HLA normalization via py-ard

    @mihaitodor
    mihaitodor committed May 16, 2024
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  25. Refactor utilities data fetching

    @mihaitodor
    mihaitodor committed May 16, 2024
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  26. Add utility for fetching and packing RefSeq data

    @mihaitodor
    mihaitodor committed May 16, 2024
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  27. Add implication identifiers 

    Also remove them from the variants
    @mihaitodor
    mihaitodor committed May 16, 2024
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  28. Use pyliftover as fallback for hgvs liftover failures

    @mihaitodor
    mihaitodor committed May 16, 2024
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