openvax / topiary / 24489421787 / 3
88%
master: 90%

LAST BUILD BRANCH: v5.16.2
DEFAULT BRANCH: master
Ran
Files 34
Run time 1s
Badge
Embed ▾
README BADGES
x

If you need to use a raster PNG badge, change the '.svg' to '.png' in the link

Markdown

Textile

RDoc

HTML

Rst
coverage: 88.244% (+0.04%) from 88.201%
24489421787.3

Pull #138

github

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

3618 of 4100 relevant lines covered (88.24%)

0.88 hits per line

Source Files on job python-3.10 - 24489421787.3