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feat: expand reference set 44→72 sequences and update discovery probability - #33
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…ity assessment - Add 29 well-characterized AMP sequences from published literature to the curated reference set, spanning LL-37 fragments (KR-12, FK-13, FK-16), cathelicidins (BMAP-27, BMAP-28, mCRAMP), proline-rich (apidaecin, oncocin, pyrrhocoricin), marine (pleurocidin, clavanin A), and engineered (WLBU2, BP100, omiganan) families — total 44 → 72 unique sequences - Remove duplicate REF-GIG-001 (identical to REF-MAG-001) - Add tests/test_reference_set.py: 14 tests guarding structure, uniqueness, canonical amino acids, family coverage (≥20 families, ≥70 sequences) - Update docs/DISCOVERY_PREDICTION.md: mark PRs #31–#32 completed, revise serum stability probability 10–20% → 25–40% based on updated pilot panel composition, revise combined "breaking news" probability 5–12% → 10–25% with root cause analysis of remaining gap
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Summary
tests/test_reference_set.pyvalidating structure (no dups, no non-canonical AAs, length range), ID uniqueness, and family coverage (≥20 families, cathelicidin/proline-rich/magainin/temporin all asserted present).Impact on scoring
The reference set expansion does not change novelty scores for current nominees (seeds are already in references — max similarity is to the seed reference, not any new entry). It improves the reference landscape for future runs with non-seed-derived candidates.
Test plan
python -m pytest tests/test_reference_set.py -v→ 14 passedpython -m pytest tests/ -q→ 872 passeddocs/DISCOVERY_PREDICTION.mdfor updated probability tables🤖 Generated with Claude Code