<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 href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br>
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    <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>
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      <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 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 href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
          wrote:<br>
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              <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>
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                <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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                    <br>
                  </div>
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</pre>
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