[ensembl-dev] Getting variation posiition relaive to the CDNA

[Graham Ritchie]

Hi Gavin,

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).

Cheers,

Graham


On 28 Feb 2011, at 12:46, Oliver, Gavin wrote:

> Hi,
>  
> 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?
>  
> Best,
>  
> Gavin
>  
>  
> The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.
>  
> Almac Group (UK) Limited, registered no. NI061368.  Almac Sciences Limited, registered no. NI041550. Almac Discovery Limited, registered no. NI046249.  Almac Pharma Services Limited, registered no. NI045055.  Almac Clinical Services Limited, registered no. NI041905.  Almac Clinical Technologies Limited, registered no. NI061202.  Almac Diagnostics Limited, registered no. NI043067.  All preceding companies are registered in Northern Ireland with a registered office address of Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK.  
>  
> Almac Sciences (Scotland) Limited, registered in Scotland no. SC154034.
>  
> Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation.  More information on the Almac Group can be found on the Almac website: www.almacgroup.com
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev