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Hi Will,<br>
<br>
Thank you for your fast answer, I forgot to ask about how to get
HGNC symbol too but I guess API solved my problem:<br>
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charset=windows-1252">
<br>
my $hgnc = $vf->$transcript->external_db('HGNC');<br>
<br>
Thanks!<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 26/01/15 13:53, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX0zc27qd02HcExBdc67EhjjB8N5tv-0Kg22cCZJo-TG2A@mail.gmail.com"
type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>You can get the strand of the transcript from the
transcript object:</div>
<div><br>
</div>
<div>(assuming $vf is a TranscriptVarationAllele object as
passed to the run method)</div>
<div><br>
</div>
<div>my $strand = $vf->transcript->strand();</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
<div><br>
</div>
<div><br>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 26 January 2015 at 11:26, Guillermo
Marco Puche <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000066" bgcolor="#FFFFFF"> Hi,<br>
<br>
I'm working on a plugin for VEP script.<br>
Usually in "run" fucntion I use a code like this to get
the variant chr, position, ref allele and var allele.<br>
<br>
my $line =
$vf->{base_variation_feature_overlap}->{base_variation_feature}->{_line};<br>
my @split_line = split ("\t", $line);<br>
$chr = $split_line[0]; <br>
$pos = $split_line[1];<br>
$ref_allele = $split_line[3];<br>
my $var_allele = $line_hash->{Allele};<br>
<br>
However for this plugin I need information about Gene in
this position, in particular the Gene strand.<br>
<br>
Is this possible to retrieve from any vep object?<br>
<br>
Thanks!<br>
<br>
Best regards,<br>
Guillermo.<br>
</div>
<br>
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</blockquote>
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