<div dir="ltr">There's some data cached on the transcript itself, this includes the HGNC symbol:<div><br></div><div><a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#technical">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#technical</a><br></div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 26 January 2015 at 13:39, Guillermo Marco Puche <span dir="ltr"><<a 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 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>
    
    <br>
    my $hgnc = $vf->$transcript->external_db('HGNC');<br>
    <br>
    Thanks!<br>
    <br>
    Regards,<br>
    Guillermo.<div><div class="h5"><br>
    <br>
    <div>On 26/01/15 13:53, Will McLaren wrote:<br>
    </div>
    <blockquote 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 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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            <br>
          </blockquote>
        </div>
        <br>
      </div>
      <br>
      <fieldset></fieldset>
      <br>
      <pre>_______________________________________________
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</pre>
    </blockquote>
  </div></div></div>

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<br></blockquote></div><br></div>