[ensembl-dev] VEP Gene strand

Will McLaren wm2 at ebi.ac.uk
Mon Jan 26 12:53:10 GMT 2015


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> 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
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150126/61d7c147/attachment.html>


More information about the Dev mailing list