8000 feat(promoterai): add PromoterAI port and veff module by kiliato · Pull Request #48 · gagneurlab/AbExp · GitHub
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feat(promoterai): add PromoterAI port and veff module - #48

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feat(promoterai): add PromoterAI port and veff module#48
kiliato wants to merge 1 commit into
gagneurlab:mainfrom
kiliato:feat/promoterai

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@kiliato
@kiliato kiliato commented Nov 4, 2026
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Summary

Adds PromoterAI to AbExp as a Python subpackage and an optional Snakemake module.

  • abexp.promoterai: variant-centred scoring with VCFTSSDataloader, plus gene-level aggregation with PromoterAIVeff
  • workflow/modules/veff/promoterai: Snakemake module, off by default behind promoterai.enabled
  • CI: adds PromoterAI to the package tests and the dry-run matrix

The model is not included. Illumina publishes it under a license agreement, so model_path must point to a local copy.

Testing

  • 61 unit tests pass with a stand-in model (tests/promoterai)
  • Scoring matches upstream PromoterAI on 1,000 variants: r = 0.9999998, with 999 of 1,000 within 1e-3

Not tested yet

  • The Snakemake module has not been run end to end on real data

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