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10 days ago
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Chain TIS prediction to epitope prediction end to end
Extends the Space from a single-model wrapper into the full pipeline the collaboration proposal describes: sequence -> TIS Transformer -> ORF typing -> MHCflurry -> candidate peptides All three stages are existing, openly-licensed tools. MHCflurry (Apache-2.0) is used rather than NetMHCpan, whose academic licence forbids redistribution and so cannot be hosted. Verified against the installed package rather than the docs, which were wrong in ways that mattered: - The FASTA-path CSV schema differs from the documented h5/GTF one. The score column is `output`, not `tis_transformer_score` -- so the previous tidy() matched no column and the cutoff slider and sorting silently did nothing. - TIS_pos is 1-based; everything here is 0-based. The conversion lives in one named function because an off-by-one shifts every reading frame and still yields a plausible protein. - Weights ship inside the wheel, so there is no download to warm. - --start_codons defaults to near-cognate (.*TG$…5278136