[ensembl-dev] VEP Flanking sequence plugin

[Guillermo Marco Puche]

Hello,

I updated the code in my git repo, and I still can't make it 
work:https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm

I still don't get why this is returning a string of type 1_41304886_C/T 
and not the rsID.

$tva->variation_feature->variation_name;


Thank you.

Best regards,
Guillermo.

On 04/23/13 16:45, Guillermo Marco Puche wrote:
> Hello,
>
> I'm developing a plugin for VEP that calculates 5' & 3' flanking 
> sequence for each rs.
>
> I've the plugin 95% completed. I'm just missing how are rs IDs called 
> on VEP.
> Looking into Enseml Variation API I've found this: 
> http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1VariationFeature.html
>
> It seems that I need VariationFeature adaptor set so I can call 
> "variation_name" method get the rs and then call 
> "five_prime_flanking_seq" & "three_prime_flanking_seq" methods to get 
> the flanking sequence.
>
> I don't know why even after changing adaptor I'm still getting 
> "2_26739423_T/C" if I'm not using TranscriptVariation adaptor but 
> VariantFeature I should be getting rsxxxxxx ID.
>
> Plugin code can be found in Github: 
> https://github.com/guillermomarco/vcf_input/blob/master/flanking_sequence.pm
>
>
>
>
> Thank you !
>
> Best regards,
> Guillermo.
>
>
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