[ensembl-dev] VEP Gene strand

[Guillermo Marco Puche]

Hi Will,

Thank you for your fast answer, I forgot to ask about how to get HGNC 
symbol too but I guess API solved my problem:

my $hgnc = $vf->$transcript->external_db('HGNC');

Thanks!

Regards,
Guillermo.

On 26/01/15 13:53, 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.
>
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