Add selenocysteine (Sec/U) regression tests (closes #42) - #401
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#42 (2015) observed varcode treating selenocysteines as stop codons, producing spurious StopLoss / UTR effects for selenoproteins. That no longer happens: varcode annotates against Ensembl's reference protein_sequence (full-length, with U at the recoded UGA) rather than re-translating the CDS with the standard table. Verified on GPX1 (ENST00000419783, Sec at residue 49) and locked in with regression tests covering the three paths: - substitution AT the Sec codon -> Substitution p.U49C (aa_ref="U"), not StopLoss/UTR; - substitution downstream -> p.R100W with correct numbering (read-through); - in-frame deletion upstream -> full-length mutant protein that retains U. Passes under both the fast and protein_diff annotators. Closes #42
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Summary
Triages and resolves #42 ("Check which apparent stop codons are actually selenocysteines", 2015).
Finding: the described bug is gone. varcode no longer treats an internal selenocysteine UGA as a stop codon. It annotates against Ensembl's reference
protein_sequence— which is full-length with aUat the recoded position — rather than re-translating the coding sequence with the standard table, so selenoprotein variants are not mis-annotated as StopLoss / UTR effects.Verification (GPX1, ENST00000419783, Sec at residue 49)
Substitution p.U49C,aa_ref="U"— missense, not StopLossp.R100W— correct numbering (read-through)UNotes
fastandprotein_diffannotators.cached_release(81)per suite convention.Closes #42
https://claude.ai/code/session_01VNtZRyKZ7u9jiMGPQEbx4c