[ensembl-dev] VEP Gene strand

Will McLaren wm2 at ebi.ac.uk
Mon Jan 26 13:56:00 GMT 2015


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> 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> 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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>
>
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