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Add specificity databases and `immvoke annotate` - #9

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annotation-dbs

Open

Add specificity databases and `immvoke annotate`#9
ssnn-airr wants to merge 51 commits into
devfrom
annotation-dbs

Commits on Aug 14, 2026
- Added initial IEDB annotation module
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  5743410
- Added initial IEDB annotation module
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  04bdfb9
- Added annotation readme
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- Add empty placeholder files for CoV-AbDab and ASD
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- Renamed annotations to specificity
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Commits on Sep 13, 2026
- Added specificity functions
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- Added specificity functions along side tests
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- Added def, fuzzy functions and revised tests
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- Revised readme
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Commits on Oct 9, 2026
- Merge origin/dev: move specificity databases under immvoke
  
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- Make symscan the default annotate backend
  
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- Run Specificity's tests in CI and fix its import order
  
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- Leave CompAIRR out of annotate's docs and help
  
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- Raise the pyarrow floor to 16
  
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Commits on Oct 14, 2026
- Prefer IEDB's calculated V/D/J-gene calls over curated ones
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- Rework annotate around a single annotateSpecificity() entry point
  
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- Split Specificity docs into usage (README) and design (idea.md)
  
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  2cdd615
- Download IEDB's own AIRR export for bcr instead of converting
  
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- Match through symscan only, with X, blank and gene-call rules
  
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  e65684b
- Drop the unused rapidfuzz dependency
  
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- Keep human receptors only from IEDB
  
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- Compare V/J-gene calls at gene level only
  
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- Rename CDR3 to CDR3H, keep IEDB's locus as is, table the workflow
  
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Commits on Oct 23, 2026
- Add annotation output bundle, scored pairs, one folder per database
  
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- Bring docs and comments in line with the output bundle and layout
  
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  d212c36
- Fix numpy options, blank cell_ids and a pandas 4 break in annotate
  
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- Score every gated pair, name outputs by database, rows by sequence_id
  
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Commits on Oct 28, 2026
- Drop IEDB's raw mirror after download, write a readable AIRR validation log
  
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- Remove the `specificity bcr` shortcut in favour of `iedb download bcr`
  
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- Add --air_species to IEDB bcr/tcr, keep every species by default
  
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- Add --outcome to IEDB bcr/tcr, replacing --qualitative_measure on bcell
  
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- Spell specificity download's own flags with underscores
  
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- Add --antigen_species to IEDB bcr/tcr, resolved live against IEDB
  
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- Name specificity outputs <db>_<table>.tsv, e.g. iedb/iedb_bcr.tsv
  
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- Drop IEDB's bcell and bcr_to_bcell tables, keep bcr and tcr only
  
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- Hash specificity rows a column at a time, fixing the slow tcr download
  
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- Make specificity search count what a table holds; group and describe filters
  
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- Add each IEDB record's antigen and its source species at download
  
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Commits on Oct 29, 2026
- Report only each query's best hits, with antigen info; add --full-dist-matrix
  
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- Add --antigen_structure_type to IEDB bcr/tcr, and its column
  
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- Make specificity download say when it starts and finishes, with stats
  
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- Leave out chains with no species recorded when --air_species is given
  
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- Let 'specificity <db> search|download all' take the filters its tables share
  
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- Add --assay_type, --disease and --paired_only to IEDB bcr/tcr
  
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- Let 'immvoke schema' work on the specificity databases
  
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- Leave query rows with no hit out of the annotation table
  
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- Remove a full matrix an earlier run left when this one wants none
  
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- Say what an annotation is comparing while it runs
  
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Commits on Oct 30, 2026
- Search one gene group at a time instead of gating afterwards
  
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- Report every compared pair in the full matrix, not only the hits
  
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- Write the annotation long, one row per hit, with a summary beside it
  
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  9ca0928

Commits

Commits on Aug 14, 2026

Commits on Sep 13, 2026

Commits on Oct 9, 2026

Commits on Oct 14, 2026

Commits on Oct 23, 2026

Commits on Oct 28, 2026

Commits on Oct 29, 2026

Commits on Oct 30, 2026