pirl-unc / tsarina / 27569652097
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coverage: 73.971%. Remained the same
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Add cancer-placenta-antigen candidates from HPA single-cell scan (LGALS16 + 3) (#125)

* Add cancer-placenta-antigen candidates from HPA single-cell scan (closes #124)

Surfaced by the pirlygenes placental-secretome analysis (HPA single-cell
trophoblast vs T-cell/somatic scan): placenta-restricted, somatic-silent at the
cell-type level, absent from the source CTA DBs. Added to add_cta_gene.py
GENE_SPECS; the bulk-consensus reproductive-restriction filter classifies each:

  LGALS16  PLACENTAL    pass  -- the missing 3rd placental galectin (LGALS13/14
                              already curated; completes the set)
  NLRP9    REPRODUCTIVE pass
  ZFP42    TESTIS       pass  -- REX1, testis-restricted on bulk consensus
  KISS1R   SOMATIC      excluded candidate (hypothalamus on bulk)
  CALHM4   SOMATIC      excluded candidate

The single-cell scan and bulk consensus disagree on KISS1R/CALHM4 -- the
established bulk filter is authoritative and correctly excludes them, exactly the
cross-check it exists to provide. CGB1/3/7 and PSG7 already in the universe
(excluded SOMATIC); not re-added. All 5 are protein-coding, full-length canonical
models (142-991 aa). CTA passing count 272->275; filtered 297->300.

Pre-existing unrelated failure: test_proteoform_groups_mirror_in_sync_with_cancerdata
fails on main too (stale cancerdata mirror from #111/#93; cancerdata sync on hold).

* Bump version for cancer-placenta-antigen additions

* Docs: correct add_cta_gene docstring re excluded candidates

The module docstring claimed every added gene is asserted to pass the
reproductive-restriction filter before writing. That contradicts the
actual behavior (and the inline comment at build_row): filter-failing
genes are recorded with passes_filters=False as excluded candidates, not
refused. Only fragment models (#108) and consensus-absent genes are
hard-refused. Surfaced by the #124 batch (KISS1R/CALHM4 -> SOMATIC).

Refs #124.

* Harden add_cta_gene validation; drop NLRP9 (... (continued)

2751 of 3719 relevant lines covered (73.97%)

0.74 hits per line

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Source Files on build 27569652097