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Support for MSA contexts and .aligned.pqt format #109

Merged
merged 36 commits into from
Oct 21, 2024
Merged

Support for MSA contexts and .aligned.pqt format #109

merged 36 commits into from
Oct 21, 2024

Commits on Oct 16, 2024

  1. Add pandera dependency

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  2. Make the fasta object a named tuple

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  3. Code to tokenize a3m style alignments

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  4. Add tests

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  5. Aligned parquet support

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  6. Example .a3m files

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  7. Readability of MSAContext

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  8. Support for more indexing on msa context

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  9. Initial implementation of loading MSA contexts

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  10. Log warnings on missing MSAs

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  11. Hooks to load MSA

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  12. Shape fixes

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  13. Cleanup

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  14. Cleanup

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  15. logging

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  16. Minor

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  17. Additional example code + docs

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  18. Fix fasta parsing giving incomplete headers

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  19. Misc. fixes

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  20. Bugfix

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  21. Always include query row when we split into rows to pair or not pair

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  22. Check

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  23. Typo fix

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  24. Add example aligned parquets

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  25. Remove unused files

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  26. Use Serialized MSA

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  27. Remove dev code

    @wukevin @arogozhnikov
    wukevin authored and arogozhnikov committed Oct 16, 2024
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  28. Update examples/msas/README.md 

    Co-authored-by: Jack Dent <[email protected]>
    @wukevin @jackdent @arogozhnikov
    2 people authored and arogozhnikov committed Oct 16, 2024
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Commits on Oct 19, 2024

  1. get rid of species logic in MSAs, del SerializedMSAForSingleSequence,

    @arogozhnikov
    arogozhnikov committed Oct 19, 2024
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  2. rm login used for debugging

    @arogozhnikov
    arogozhnikov committed Oct 19, 2024
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Commits on Oct 20, 2024

  1. update readme, misc. small changes

    @wukevin
    wukevin committed Oct 20, 2024
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  2. Do not truncate MSAs used for MSA profile

    @wukevin
    wukevin committed Oct 20, 2024
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  3. Rename main msa context -> profile msa context; do not check its depth

    @wukevin
    wukevin committed Oct 20, 2024
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  4. Rename function

    @wukevin
    wukevin committed Oct 20, 2024
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Commits on Oct 21, 2024

  1. Make ukey pairing sort by sequence identity first

    @wukevin
    wukevin committed Oct 21, 2024
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  2. Logging for pairing

    @wukevin
    wukevin committed Oct 21, 2024
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