openvax / topiary / 24372442691

88%

master: 90%

Build Type

Pull #121

github

Committed by iskandr

Commit Message

Refactor predict_from_variants onto AntigenFragment (PR B)

predict_from_mutation_effects now builds a list of AntigenFragments
from varcode effects and delegates to predict_from_antigens, replacing
the parallel per-row metadata loop. The variant path gains the
fragment-derived columns (fragment_id, source_type, overlaps_target,
wt_peptide) for free while preserving the legacy column contract
(absolute peptide_offset, mutation_start/end_in_peptide, transcript_name).

- Added transcript_name field on AntigenFragment + io_antigen.py schema.
- New _fragment_from_effect helper slices a subsequence around the
  mutation and populates reference_sequence only for length-matched
  (substitution-compatible) effects.
- _add_legacy_mutation_columns rebases peptide_offset to absolute
  protein coords and derives mutation_start/end_in_peptide from the
  fragment's target_intervals.
- Deleted the row-by-row extra_columns bookkeeping and the variant_
  string_to_*_dict scaffolding.
- 13 new regression tests covering the legacy column contract and
  _fragment_from_effect directly.

Pull Request Pull Request #121: Refactor predict_from_variants onto AntigenFragment (PR B)

Coverage Stats

70 of 79 new or added lines in 2 files covered. (88.61%)

14 existing lines in 2 files now uncovered.

3007 of 3419 relevant lines covered (87.95%)

2.64 hits per line