[ensembl-dev] VEP Flanking sequence plugin

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Tue Apr 23 15:45:21 BST 2013


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.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130423/c52d4184/attachment.html>


More information about the Dev mailing list