[ensembl-dev] VEP Gene strand

[Michael Maguire]

thanks Kieron, how about this afternoon @2:30?
Cheers

Mick

On 26/01/2015 12:53, Will McLaren wrote:
> Hi Guillermo,
>
> You can get the strand of the transcript from the transcript object:
>
> (assuming $vf is a TranscriptVarationAllele object as passed to the 
> run method)
>
> my $strand = $vf->transcript->strand();
>
> Regards
>
> Will McLaren
> Ensembl Variation
>
>
>
> On 26 January 2015 at 11:26, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     Hi,
>
>     I'm working on a plugin for VEP script.
>     Usually in "run" fucntion I use a code like this to get the
>     variant chr, position, ref allele and var allele.
>
>     my $line =
>     $vf->{base_variation_feature_overlap}->{base_variation_feature}->{_line};
>     my @split_line = split ("\t", $line);
>     $chr = $split_line[0];
>     $pos = $split_line[1];
>     $ref_allele = $split_line[3];
>     my $var_allele = $line_hash->{Allele};
>
>     However for this plugin I need information about Gene in this
>     position, in particular the Gene strand.
>
>     Is this possible to retrieve from any vep object?
>
>     Thanks!
>
>     Best regards,
>     Guillermo.
>
>     _______________________________________________
>     Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>     Posting guidelines and subscribe/unsubscribe info:
>     http://lists.ensembl.org/mailman/listinfo/dev
>     Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-- 
Michael Maguire

Bioinformatics Data Manager
CTTV Core Database Team
Centre for Therapeutic Target Validation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

Phone +44 1223 494674
Email mmaguire at ebi.ac.uk

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150126/d4dc277c/attachment.html>