openvax / topiary
90%
master: 90%

LAST BUILD BRANCH: v5.16.2
DEFAULT BRANCH: master
Repo Added
Files 35
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

LAST BUILD ON BRANCH v5.13.0
branch: v5.13.0
CHANGE BRANCH
x

coverage: 89.526% (-0.07%) from 89.595%
25673003453

push

github

web-flow 
Add best-allele aggregation for haplotype-mode presentation (#158) (#160)

* Add best-allele aggregation accessors for haplotype-mode predictors

Issue #158 calls out that pMHC_presentation from haplotype-mode
predictors (MHCflurry's class1_presentation in haplotype mode) is
conceptually a multi-allele input → per-peptide answer, but mhctools
emits one row per (peptide, allele) so the DSL's per-allele grouping
returns per-allele scores by default. Add an explicit aggregator that
returns the best score across alleles plus the corresponding allele
attribution, gated behind new accessors so the default per-allele
behavior is preserved.

- BestAlleleField DSLNode: per-peptide max/min of (kind, field) across
  alleles, broadcast back to ctx.group_index. Direction by field:
  score=max, value=min, percentile_rank=min.
- KindAccessor properties: best_value, best_score, best_rank, plus
  *_allele variants returning the allele name string.
- DSL string parser: presentation['mhcflurry'].best_score and
  best_score_allele (and rank/value/percentile spellings) now parse to
  BestAlleleField.
- Refactor: factor _filter_kind_method_version helper out of Field.eval
  for reuse by BestAlleleField.
- Bump topiary to 5.12.0 (additive minor).

Use case (per #158): vaxrank's "presented anywhere" tier signal —
``Presentation['mhcflurry'].best_score`` returns the multi-allele
aggregate, ``best_score_allele`` returns the attribution.

* Address review: drop merge, per-kind directions, kind_support warnings

Four fixes against PR #160 review:

1. Replace the fragile ``__best__``/merge broadcast with
   ``ctx.group_index.droplevel('allele')`` + ``per_peptide.reindex()``.
   No intermediate `__best__` column, no positional-merge ordering
   assumption, fewer allocations. ``sub.copy()`` is gone too — work
   on the filter's already-fresh slice via index masks + ``.assign()``.

2. Replace the field-only ``_BEST_DIRECTIONS`` constant with a
   per-(kind, field) lookup ``_best_dir... (continued)

147 of 164 new or added lines in 4 files covered. (89.63%)

4214 of 4707 relevant lines covered (89.53%)

2.69 hits per line

Relevant lines Covered
4707 RELEVANT LINES 4214 COVERED LINES
2.69 HITS PER LINE
Source Files on v5.13.0

Recent builds

Builds Branch Commit Type Ran Committer Via Coverage
25673003453 v5.13.0 Add best-allele aggregation for haplotype-mode presentation (#158) (#160) * Add best-allele aggregation accessors for haplotype-mode predictors Issue #158 calls out that pMHC_presentation from haplotype-mode predictors (MHCflurry's class1_presen... push web-flow github
89.53
See All Builds (269)