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seqtree v0.0.3

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@mikessh mikessh released this 20 Jun 21:04
· 77 commits to master since this release
v0.0.3
5bfa7a1

seqtree v0.0.3 — pMHC epitope search, position-aware scoring, KmerIndex, MHC-allele guessing, and a reproducible benchmark pipeline.

Highlights since v0.0.2:

  • pMHC epitope homology layer (anchor-masked k-mers, mimics, allele assignment) and C++ KmerIndex seed-and-gather.
  • Position-aware scoring (PositionalMatrix) and local mode.
  • Control-set E-values with Elhanati selection factor; MHC-I/II ROC-PR guessing benchmark + non-binder filter.
  • PAM50 + custom (Gram-distance) substitution matrices; seqtm collision metric.
  • Reproducible benchmark pipeline: deterministic table producers (shell+python) → plot scripts → committed oracle, with CI oracle-diff and time/memory regression checks.

Wheels (cp310–cp313; Linux x86-64, macOS arm64, Windows x86-64) and the sdist are published to PyPI by the Publish workflow.

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