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thanks Kieron, how about this afternoon @2:30?<br>
Cheers<br>
<br>
Mick<br>
<br>
<div class="moz-cite-prefix">On 26/01/2015 12:53, 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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<br>
<pre class="moz-signature" cols="72">--
Michael Maguire
Bioinformatics Data Manager
CTTV Core Database Team
Centre for Therapeutic Target Validation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
Phone +44 1223 494674
Email <a class="moz-txt-link-abbreviated" href="mailto:mmaguire@ebi.ac.uk">mmaguire@ebi.ac.uk</a></pre>
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