openvax / topiary / 24490120150

88%

master: 90%

Build Type

Pull #138

github

Committed by iskandr

Commit Message

Add BLOSUM62 distance metric to SelfProteome.nearest

Default metric is now "blosum62" — conservative substitutions (I↔L,
BLOSUM62 score +2) produce lower distances than non-conservative
(I↔W, score -3).  BLOSUM62 matrix loaded lazily from Biopython at
first use, not hardcoded.

metric="hamming" (count mismatches) kept as opt-in.

New output column: self_nearest_blosum_distance (only present when
metric="blosum62").  self_nearest_edit_distance (Hamming) is always
computed regardless of metric since it's useful for threshold-based
filtering.

5 new tests covering exact-match zero, conservative vs radical sub
ordering, tie-breaking preference for conservative over radical when
both are Hamming-1, hamming opt-in, invalid metric error.

34 self_proteome tests pass, lint clean.

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

Coverage Stats

70 of 71 new or added lines in 1 file covered. (98.59%)

13 existing lines in 1 file now uncovered.

3650 of 4132 relevant lines covered (88.33%)

2.65 hits per line