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Totally forgot about that!<br>
Thank you so much.<br>
<br>
Regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 26/01/15 14:56, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX1OYreotgfNyG0AWvw_f2fyyW+e6m_AJhZyZu+2iwXPrw@mail.gmail.com"
type="cite">
<div dir="ltr">There's some data cached on the transcript itself,
this includes the HGNC symbol:
<div><br>
</div>
<div><a moz-do-not-send="true"
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 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 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
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>
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