openvax / topiary / 24489421787

88%

master: 90%

Build Type

Pull #138

github

Committed by iskandr

Commit Message

Add scope="protected_tissues" to SelfProteome (part B of #124)

Filters the reference proteome to genes expressed in named tissues —
the cross-reactivity-relevant subset of self.

## Multi-species design

Three paths, ordered by specificity:

1. **Explicit gene set** (any species): pass
   tissue_gene_ids={gene_ids} with pre-computed gene IDs (e.g. from
   Tabula Muris for mouse, or custom RNA-seq for dog).  Bypasses
   pirlygenes entirely.  tissues= and min_tissue_ntpm= ignored.

2. **Human default**: queries pirlygenes via
   topiary.sources.tissue_expressed_gene_ids with the requested
   tissue list (defaults to curated vital-organ set: heart_muscle,
   lung, liver, kidney, cerebral_cortex) and min_ntpm threshold.

3. **Non-human without tissue_gene_ids**: raises ValueError with an
   actionable message explaining that pirlygenes tissue data is
   human-only and directing users to supply tissue_gene_ids=.

## Version string

- Explicit gene set: "protected_tissues+gene_ids-sha256:{hash}"
- Human default: "protected_tissues+tissues-{list}+min_ntpm-{value}"

## Tests

4 new tests:
- Non-human without tissue_gene_ids raises.
- Non-human with explicit gene_ids works (mocked pyensembl).
- Human with default tissues works (mocked pirlygenes via monkeypatch).
- Human with custom tissues list works.

Old test_protected_tissues_not_yet_implemented updated to test the
non-human error path instead (the NotImplementedError is gone).

Full suite 1170 pass (up from 1166), lint clean.

Pull Request Pull Request #138: SelfProteome scope="protected_tissues" — multi-species (part B of #124)

Coverage Stats

64 of 74 new or added lines in 1 file covered. (86.49%)

12 existing lines in 1 file now uncovered.

3618 of 4100 relevant lines covered (88.24%)

2.65 hits per line