[ensembl-dev] Getting variation posiition relaive to the CDNA
grsr at ebi.ac.uk
Mon Feb 28 13:05:19 GMT 2011
You can either create a TranscriptVariation object representing the combination of VariationFeature and a Transcript and use the cdna_start and cdna_end methods from this class, or if you want to work with VariationFeatures directly you can use the TranscriptMapper from the core API to map between the genomic coordinates of a VariationFeature and the cDNA coordinates of your transcript (which is how cdna_start and cdna_end work internally).
On 28 Feb 2011, at 12:46, Oliver, Gavin wrote:
> To get variation positions relative to a transcript I do
> my $transcript_slice = $slice_adaptor->fetch_by_transcript_stable_id($transcript_id);
> my $variataion_start = $transcript_variation->variation_feature->transfer($transcript_slice)->start;
> But I am wondering how to get the same positions for the cdna?
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