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<div class="moz-cite-prefix">Hello,<br>
<br>
I fixed it by downloading fresh Conservation plugin from VEP
Github too.<br>
Someone pushed a commit into my local repository and modified
badly the script. That's why no conservation score was appearing.<br>
<br>
Thank you and sorry for inconvenience.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
On 10/15/2013 09:09 AM, James Walker wrote:<br>
</div>
<blockquote
cite="mid:CAFrYFReCiBhAfB-pS4SVF=Oz24RoRE==r=Mca6hmq67fKiTRPw@mail.gmail.com"
type="cite">
<div dir="ltr">I did a fresh install of API + Plugins directory.<br>
Works fine now, thank you Will.
<div><br>
</div>
<div>Regards,</div>
<div>James.</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/10/14 James Walker <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:walker.james.kerrigan@gmail.com"
target="_blank">walker.james.kerrigan@gmail.com</a>></span><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've installed API from <a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/api_installation.html"
target="_blank">http://www.ensembl.org/info/docs/api/api_installation.html</a></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 moz-do-not-send="true"
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,
<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 moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/api_cvs.html"
target="_blank">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 moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/api/api_installation.html"
target="_blank">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>
<span><font color="#888888">
<div><br>
</div>
<div>Will</div>
</font></span></div>
<div>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">
On 14 October 2013 16:07, James Walker <span
dir="ltr"><<a moz-do-not-send="true"
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>
</span></div><div style="padding-left:10px"><span>to </span></div>
<div style="padding-left:10px"><span>
</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>
</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>
<div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">2013/10/14
Will McLaren <span dir="ltr"><<a
moz-do-not-send="true"
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
moz-do-not-send="true"
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>
</pre>
</blockquote>
<blockquote
type="cite">
<pre>
</pre>
<pre><span style="font-family:arial">James.</span></pre>
</blockquote>
</div>
</div>
<br>
</div>
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