openvax / vaxrank / 25565656451
96%
master: 88%

LAST BUILD BRANCH: v3.1.8
DEFAULT BRANCH: master
Ran
Jobs 0
Files 0
Run time –
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
25565656451

push

github

web-flow 
PeptideContext + CandidateEpitope: multi-axis per-peptide model (Phase 1) (#283)

* PeptideContext + CandidateEpitope: multi-axis, comparator-driven per-peptide model

Introduces vaxrank/peptide_context.py as the replacement shape for the flat
EpitopePrediction. Two layers:

  PeptideContext  — peptide sequence + flanks + provenance + tuple of
                    mhctools.Prediction records (kind / predictor / allele).
  CandidateEpitope — mutant PeptideContext + open-ended comparators dict
                    (wt today; nearest_self / nearest_vital_self /
                    nearest_nonCTA / nearest_oncovirus reserved for #254 /
                    #257 / #258).

Why: the flat EpitopePrediction can only hold one axis (affinity
percentile_rank), which is exactly the gap that #282 documents — the
2.25.0 coverage feature's "two-axis evidence" story is half-real because
presentation_percentile has nowhere to land. Generalizing to mhctools'
multi-kind Prediction record fixes that cleanly and gives us the shape
we need for the upcoming safety / homology comparators.

Disambiguation contract: best_for_kind(kind, *, predictor=None) raises
ValueError when multiple predictors emitted that kind and no predictor
arg is given — cross-predictor max(score) is meaningless because each
predictor's score scale is its own. Callers that want a per-predictor
loop iterate predictors_for_kind() explicitly.

Phase 1 only: types + tests. Migration of the existing call-sites
(epitope_io / epitope_logic / coverage / report) lands in follow-up PRs.

Refs: #282, #254, #257, #258, #261.

* PeptideContext.best: kind aliases + version disambiguation

Renames best_for_kind → best, with two behavioral additions:

1. Kind aliases. mhcflurry / netmhcpan / pVACseq / LENS shorthand
   resolves to canonical mhctools.Prediction.kind strings:
     ba / affinity / binding         → pMHC_affinity
     el / presentation / elution     → pMHC_presentation
     stability / cleavage / proteasome /... (continued)
Source Files on build 25565656451
Detailed source file information is not available for this build.