Fix method codon() in TranscriptVariationAllele #1131
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dglemos
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likhitha-surapaneni
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Nov 25, 2024
likhitha-surapaneni
merged commit 65d9663
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Ensembl:postreleasefix/114
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@likhitha-surapaneni I have the same error as Ensembl/ensembl-vep#1775 on the ensembl rest api in the variant_recorder (http://rest.ensembl.org/variant_recoder/human/rs201618914) Is this fix also a fix for that? And when does this fix is expected to land in the rest api infra? Thank you. |
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The fix has landed in the rest api infra. |
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The method to calculate the codon was updated in release 113 - check this PR.
After this update, the
CodonsandConsequenceare wrong for some RefSeq transcripts.Check ticket: https://www.ebi.ac.uk/panda/jira/browse/ENSVAR-6640
The line
substr($cds, $tv->cds_start(undef, $tr->strand * $shifting_offset) -1, $vf_nt_len) = $seq;has been removed from the method but it is important for these RefSeq transcripts.This code edits the
$cdsat the specific position start and end ($tv->cds_start(undef, $tr->strand * $shifting_offset) -1, $vf_nt_len). It replaces the allele by $seq.This code update should be cherry-picked to 113.
It should fix the following issues:
Ensembl/ensembl-vep#1775
Ensembl/ensembl-vep#1787
Ensembl/ensembl-vep#1793