26984084988
71%

Ran 04 Jun 2026 10:46PM UTC

Jobs 1

Files 35

Run time 1min

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Committed 04 Jun 2026 10:45PM UTC coverage: 71.104% (+0.2%) from 70.875%

Build # 26984084988

Build Type

push

github

Committed by

web-flow

Commit Message

Backfill CTA Aliases from NCBI; add cta_symbol_for_alias resolution (#77) (#87)

The Aliases column was ~96% empty, so lookups by common antigen names silently
missed (NY-ESO-1, CT12.2, MAGE/GAGE historical symbols).

- Populate Aliases for every gene from NCBI gene_info synonyms (matched by
  Ensembl gene ID), merged with existing curated aliases + a small colloquial
  supplement NCBI omits (NY-ESO-1). 310/360 genes now carry aliases (was 19).
- Add cta_symbol_for_alias(name): case/punctuation-insensitive resolution of a
  CTA name or synonym to its official symbol. NY-ESO-1 / ESO1 -> CTAG1B (the
  cloned paralog) via a small canonical-override map; unknown names -> None.
- Make the curation scripts durable artifacts: scripts/cta_sources.py downloads
  + caches the HPA consensus and NCBI gene_info on demand, so add_xage2.py,
  add_cta_gene.py and backfill_aliases.py are self-contained and reproducible
  (no manual /tmp setup). Cache is gitignored.

Tests + docs added. Version 1.4.5 -> 1.4.6.

Coverage Stats

2441 of 3433 relevant lines covered (71.1%)

0.71 hits per line

Coverage Regressions

Lines	Coverage	∆	File
3	97.35	0.83%	gene_sets.py

Jobs

ID	Job ID	Ran	Files	Coverage
1	26984084988.1	04 Jun 2026 10:46PM UTC	35	71.1	GitHub Action Run

pirl-unc / tsarina / 26984084988
71%

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pirl-unc / tsarina / 26984084988 71%

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pirl-unc / tsarina / 26984084988
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