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Add MixTCRpred model catalog and wrapper - #275

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iskandr merged 2 commits into
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feature/mixtcrpred
Sep 5, 2026
Merged

Add MixTCRpred model catalog and wrapper#275
iskandr merged 2 commits into
masterfrom
feature/mixtcrpred

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@iskandr

@iskandr iskandr commented Sep 5, 2026

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Summary

  • extend TCR with backward-compatible paired-chain V/J fields and common upstream column aliases
  • add a pinned, license-gated MixTCRpred source fetch plus selective checksum-verified Zenodo model downloads
  • expose the full 147-target model catalog in Python and through mhctools ls mixtcrpred --models, including shipped and optional weights, paths, managers, provenance, training counts, AUCs, and confidence tier
  • add fixed-pMHC prediction APIs and a CSV CLI that preserve raw score, percentile rank, corrected V/J genes, V-derived CDR1/2 loops, and QC warnings
  • exercise an upstream checkpoint on a current PyTorch/Lightning CPU stack in dedicated CI
  • document why small CALIS parameters stay packaged and why DTU identity-bound registrations cannot be automated by --accept-license

The released MixTCRpred network consumes paired CDR3s and V-derived CDR1/2. J genes are accepted, corrected, and reported for schema completeness, but they are not network inputs.

Closes #230.
Related: #274.
Upstream runtime report: GfellerLab/MixTCRpred#10

Verification

  • ./lint.sh
  • ./test.sh — 734 passed, 56 skipped, 2 xfailed
  • live current-runtime regression — 13 passed, including the real bundled checkpoint
  • clean managed fetch, optional Zenodo download, checksum/provenance manifest, catalog listing, and the official 1,003-row example reproduced locally

@iskandr
iskandr merged commit e679973 into master Sep 5, 2026
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@iskandr
iskandr deleted the feature/mixtcrpred branch September 5, 2026 02:53
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Add MixTCRpred pMHC:TCR binding predictor wrapper

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