<div dir="ltr">Hi James,<div><br></div><div>If you used CVS to install the ensembl-compara API module, then if you don't specify a branch number when you checkout the code, by default CVS will fetch the bleeding-edge or "head" code, which is not intended for external use.</div>
<div><br></div><div>On the instructions on this page:</div><div><br></div><div><a href="http://www.ensembl.org/info/docs/api/api_cvs.html">http://www.ensembl.org/info/docs/api/api_cvs.html</a><br></div><div><br></div><div>
if you miss off the "-r branch-ensembl-73" in your CVS checkout command, you will get head code.</div><div><br></div><div>If you have installed from the tar.gz archives (as per <a href="http://www.ensembl.org/info/docs/api/api_installation.html">http://www.ensembl.org/info/docs/api/api_installation.html</a>) then you won't be at risk of this.</div>
<div><br></div><div>The change you have made to the plugin code won't make any difference, it just suppresses a warning from the VEP.</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">
On 14 October 2013 16:07, James Walker <span dir="ltr"><<a href="mailto:walker.james.kerrigan@gmail.com" target="_blank">walker.james.kerrigan@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hello Will,<div><br></div><div>I'm using vep cache plus local ensembl database to annotate variants.</div><div><br></div><div>I don't really understand what do you refer with: "<span style="font-family:arial,sans-serif;font-size:13px">Is there any chance you have accidentally checked out head code (instead of branch 73) for the ensembl-compara API?"</span></div>
<div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">I've modified code in the script from:</span></div><div><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div><div><pre style="font-family:Consolas,'Liberation Mono',Courier,monospace;font-size:12px;margin-top:0px;margin-bottom:0px;color:rgb(51,51,51);line-height:17.99715805053711px"><div style="padding-left:10px">
<span style="font-weight:bold">sub </span><span style="color:rgb(153,0,0);font-weight:bold">version</span> <span>{</span></div><div style="padding-left:10px"> <span style="font-weight:bold">return</span> <span style="color:rgb(221,17,68)">'2.3'</span><span>;</span></div>
<div style="padding-left:10px"><span>}</span></div><div style="padding-left:10px"><span><br></span></div><div style="padding-left:10px"><span>to </span></div>
<div style="padding-left:10px"><span><br></span></div><div style="padding-left:10px"><span><pre style="font-family:Consolas,'Liberation Mono',Courier,monospace;margin-top:0px;margin-bottom:0px;line-height:17.99715805053711px">
<div style="padding-left:10px"><span style="font-weight:bold">sub </span><span style="color:rgb(153,0,0);font-weight:bold">version</span> <span>{</span></div><div style="padding-left:10px">
<span style="font-weight:bold">return</span> <span style="color:rgb(221,17,68)">'73'</span><span>;</span></div><div style="padding-left:10px"><span>}</span></div>
<div style="padding-left:10px"><span><br></span></div><div style="padding-left:10px"><span>Regards,</span></div><div style="padding-left:10px">James.</div>
</pre></span></div></pre></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><br><div class="gmail_quote">2013/10/14 Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span><br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi James, Guillermo,<div><br></div><div>We're struggling to recreate the problem at our end.</div><div><br></div><div>While we do still see the warning message (which will disappear in 74 as Matthieu says), the plugin seems to be working fine.</div>
<div><br></div><div>I've tested it on the example.vcf supplied with the VEP and a larger set of ~3500 exonic variants from the 1000 genomes project, and I see Conservation scores in the output for every variant in my test set.</div>
<div><br></div><div>Are you seeing any other error messages? Are you using a local database copy, or relying on the ensembldb connection (the default when using VEP)?</div><div><br></div><div>Is there any chance you have accidentally checked out head code (instead of branch 73) for the ensembl-compara API?</div>
<div><br></div><div><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">MethodLinkSpeciesSet is not deprecated, although a couple of deprecated methods in it were removed in 73, though these are not used by the plugin.</span><br>
</div><div><span style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">Some more information would be useful!</span></div>
<div><span style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">Thanks</span></div><div><span style="font-family:arial,sans-serif;font-size:12.727272033691406px"><br>
</span></div><div><span style="font-family:arial,sans-serif;font-size:12.727272033691406px">Will</span></div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div>On 14 October 2013 15:10, James Walker <span dir="ltr"><<a href="mailto:walker.james.kerrigan@gmail.com" target="_blank">walker.james.kerrigan@gmail.com</a>></span> wrote:<br>
</div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div dir="ltr"><div lang="x-western"><blockquote type="cite"><pre><span style="font-family:arial">I'm experiencing the exact same problem. Plugin seems to be broken.</span><br>
</pre>
</blockquote><blockquote type="cite"><pre><br></pre><pre><span style="font-family:arial">James.</span></pre></blockquote></div></div>
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