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fix: Sec and Stop coincide in SEPHS2 #214

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merged 2 commits into from
Dec 9, 2024
Merged

fix: Sec and Stop coincide in SEPHS2 #214

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d8b8017
fix: Sec and Stop coincide in SEPHS2
tedil Dec 9, 2024
011e6f5
Merge remote-tracking branch 'origin/main' into fix-sec-stop-cases
tedil Dec 9, 2024
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14 changes: 13 additions & 1 deletion src/mapper/altseq.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -156,7 +156,19 @@ impl AltTranscriptData {
) -> Result<Self, Error> {
let transcript_sequence = seq.to_owned();
let aa_sequence = if !seq.is_empty() {
let seq_cds = &transcript_sequence[((cds_start - 1) as usize)..];
// In case of SEPHS2 / HGNC:19686, the last amino acid is both a selenocysteine
// and a stop codon.
// We handle this by explicitly truncating the sequence at the Sec + stop codon.
// This heuristic may not always be correct;
// alternatively/additionally, we could check `protein_accession` for known cases.
let seq_cds = if translation_table == TranslationTable::Selenocysteine
&& ref_aa_sequence.ends_with('U')
{
&transcript_sequence[((cds_start - 1) as usize)..cds_stop as usize]
} else {
&transcript_sequence[((cds_start - 1) as usize)..]
};

let seq_aa = if variant_start_aa.is_some() {
translate_cds(seq_cds, false, "X", translation_table)?
} else {
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