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<div class="moz-cite-prefix">Ok I'm gonna give it a shot.<br>
I installed latest API downloaded from Ensembl website on friday
(10/05/2013) and I'm using a local Ensembl 71 database for VEP, no
cache.<br>
<br>
Best regards,<br>
Guillermo<br>
<br>
On 05/13/2013 01:45 PM, Will McLaren wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX19agczjuKajunb+b373fKxa2qPikr8yy_1WDf=uPCikA@mail.gmail.com"
type="cite">
<div dir="ltr">There was a bug in --domains when using the cache
that has been recently fixed.
<div><br>
</div>
<div style="">Try updating your API and see if that's any
better.</div>
<div style=""><br>
</div>
<div style="">Will</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 13 May 2013 12:38, 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 bgcolor="#FFFFFF" text="#000066">
<div>Hello Will,<br>
<br>
Yes I'm currently running VEP with --domains flag. It
always shown empty for the testings for different
samples I've done until now.<br>
So domains flag is supposed to display the Interpro_ac
for overlapping protein domains?<br>
<br>
Best regards,<br>
Guillermo.
<div>
<div class="h5"><br>
<br>
On 05/13/2013 01:34 PM, Will McLaren wrote:<br>
</div>
</div>
</div>
<div>
<div class="h5">
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
Have you tried the --domains flag in the VEP?</div>
<div><br>
</div>
<div>Perhaps this is not enough information for
you but it does provide the display label of
overlapping protein domains.</div>
<div><br>
</div>
<div>The protein object is referred to as a
translation object in the Ensembl API; you can
retrieve it from the transcript via
$transcript->translation.</div>
<div><br>
</div>
<div>See <a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation.html"
target="_blank">http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Translation.html</a></div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 13 May 2013 12:15,
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 bgcolor="#FFFFFF" text="#000066">
<div>Hello,<br>
<br>
So it seems nobody has done this yet. I'll
do it then :)<br>
<br>
Does VEP support any kind of
"""Proteinfeature"""? Checking the other
scripts it seems I must be using
Transcript feature_type. <br>
<br>
Correct me if I'm wrong please, I'm a bit
confused since interpro_ac is part from
Core ProteinFeature.
(EnsEMBL::ProteinFeature::interpro_ac)<br>
<br>
Best regards,<br>
Guillermo.
<div>
<div><br>
<br>
On 05/09/2013 04:16 PM, Guillermo
Marco Puche wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div> Hello,<br>
<br>
Does anyone coded a plugin to obtain
InterPro ID and description for VEP?<br>
I've looked in VEP repo without luck.<br>
<br>
I want to know before start coding.<br>
<br>
Thank you !<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
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