Import native Exacto evidence and optional fragments - #438
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iskandr
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feat/orf-evidence-reconciliation
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September 29, 2026 19:11
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coverage: 93.366% (+0.02%) from 93.345% — feat/native-exacto-ingestion into master |
This was referenced Sep 29, 2026
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Add
read_exactofor native peptide-variant, primary-structure and translation TSVs, plus optionalread_exacto_fragmentsfor explicit new-window scanning. The pinned Exacto 0.4.6 corpus covers 228 peptides, six primary structures and 77 translations.The reader retains native records and DNA/RNA links, validates codons and peptide occurrences, preserves partial ORFs and unknown specificity, and keeps read membership transcript-scoped. Exacto's files have no HLA assignments or pMHC measurements, so import adds evidence without inventing candidates or scores. Varcode remains lazily imported (#439).
Composed workflows combine native Exacto with LENS/pVACseq files without prediction, preserve long/wide CSV/TSV evidence and ranking, exercise additive rescoring, and demonstrate that novelty intervals affect optional fragment scanning. Document supported schemas, coordinates, provenance and unsupported input.
Validation: lint, strict docs, all PR/master CI and published Vaxrank integration pass. Clean-master release gate: 4,862 passed, zero failures/skips, 35 non-pandas warnings, 94% coverage, with one local worker. All 45 focused native/lazy-import checks pass under pandas 3. Published wheel/sdist hashes and the release tag are verified.
Released as Topiary 5.88.0. Closes #365 and #439. Builds on #436 / 5.87.0.