[ensembl-dev] VEP Gene strand

[Guillermo Marco Puche]

Totally forgot about that!
Thank you so much.

Regards,
Guillermo.

On 26/01/15 14:56, Will McLaren wrote:
> There's some data cached on the transcript itself, this includes the 
> HGNC symbol:
>
> http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#technical
>
> Will
>
> On 26 January 2015 at 13:39, Guillermo Marco Puche 
> <guillermo.marco at sistemasgenomicos.com 
> <mailto:guillermo.marco at sistemasgenomicos.com>> wrote:
>
>     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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