<div dir="ltr">Hi Guillermo,<div><br></div><div>I suspect the issue is to do with database connections.</div><div><br></div><div>If you are running your plugin with the VEP in offline mode (--offline), then you will be unable to retrieve data from the databases without instantiating your own registry instance and adaptors within the plugin.</div><div><br></div><div>If you are running the VEP using --cache or --database you shouldn't have this issue; just make sure that your cache version and the version of the database you are connecting to match, and that the assemblies also match.</div><div><br></div><div>If I run, for example:</div><div><br></div><div>perl -I vep_plugins/ <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> -cache -port 3337 -dir ~/.vep/77/GRCh37/ -force -i example_GRCh37.vcf -plugin Interpro_fixed<br></div><div><br></div><div>it runs without an issue. Or similarly for the GRCh38 example:</div><div><br></div><div>perl -I vep_plugins/ <a href="http://variant_effect_predictor.pl">variant_effect_predictor.pl</a> -cache -dir ~/.vep/77/ -force -i example_GRCh38.vcf -plugin Interpro_fixed<br></div><div><br></div><div>In both these cases the VEP will use <a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a> to retrieve data; the first example uses port 3337 to connect to the GRCh37 mirror, and the second the default (3306) port to connect to the latest GRCh38 mirror.</div><div><br></div><div>HTH</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 3 October 2014 16:20, Guillermo Marco Puche <span dir="ltr"><<a 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">
Dear developers,<br>
<br>
I'm experiencing some VEP plugin errors on Ensembl 76+.<br>
<br>
I've uploaded both plugins failing to this public repository:
<a href="https://github.com/guillermomarco/vep_plugins" target="_blank">https://github.com/guillermomarco/vep_plugins</a><br>
<br>
I've been looking for API changes in
<a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1BaseVepPlugin.html#a2d966d465a2bbc2a067417cc4978e304" target="_blank">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Utils_1_1BaseVepPlugin.html#a2d966d465a2bbc2a067417cc4978e304</a>
but I can't really find why I'm getting the following errors:<br>
<br>
<pre>Plugin 'Interpro_fixed' went wrong: Can't call method "translation" on an undefined value at Interpro_fixed.pm line 107</pre>
<pre>Plugin 'Gene_description' went wrong: Can't call method "description" on an undefined value at Gene_description.pm line 78.
</pre>
It's like hashes are empty:<br>
<br>
<table>
<tbody>
<tr>
<td style="padding:0px 10px;font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="color:rgb(0,128,128)">$gene</span> <span style="font-weight:bold">=</span>
<span style="color:rgb(0,128,128)">$config</span><span style="font-weight:bold">-></span><span>{</span><span style="color:rgb(51,51,51)">ga</span><span>}</span><span style="font-weight:bold">-></span><span style="color:rgb(51,51,51)">fetch_by_transcript_stable_id</span><span>(</span><span style="color:rgb(0,128,128)">$transcript_id</span><span>);</span></td>
</tr>
<tr>
<td style="padding:0px 10px;width:50px;min-width:50px;font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;font-size:12px;line-height:18px;color:rgba(0,0,0,0.298039);vertical-align:top;text-align:right;border-style:solid;border-color:rgb(238,238,238);border-width:0px 1px 0px 0px"><br>
</td>
<td style="padding:0px 10px;font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="color:rgb(0,128,128)">$gene_desc</span> <span style="font-weight:bold">=</span>
<span style="color:rgb(0,128,128)">$gene</span><span style="font-weight:bold">-></span><span style="color:rgb(51,51,51)">description</span><span>;</span></td>
</tr>
</tbody>
</table>
<br>
<table>
<tbody>
<tr>
<td style="padding:0px 10px;font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="font-weight:bold">my</span> <span style="color:rgb(0,128,128)">$slice_adaptor</span>
<span style="font-weight:bold">=</span> <span style="color:rgb(0,128,128)">$config</span><span style="font-weight:bold">-></span><span>{</span><span style="color:rgb(51,51,51)">reg</span><span>}</span><span style="font-weight:bold">-></span><span style="color:rgb(51,51,51)">get_adaptor</span><span>((</span><span style="color:rgb(0,128,128)">$config</span><span style="font-weight:bold">-></span><span>{</span><span style="color:rgb(51,51,51)">species</span><span>}),</span> <span style="color:rgb(223,80,0)">'core'</span><span>,</span> <span style="color:rgb(223,80,0)">'Transcript'</span><span>);</span></td>
</tr>
<tr>
<td style="padding:0px 10px;width:50px;min-width:50px;font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;font-size:12px;line-height:18px;color:rgba(0,0,0,0.298039);vertical-align:top;text-align:right;border-style:solid;border-color:rgb(238,238,238);border-width:0px 1px 0px 0px"><br>
</td>
<td style="padding:0px 10px;font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="font-weight:bold">my</span> <span style="color:rgb(0,128,128)">$tr</span> <span style="font-weight:bold">=</span> <span style="color:rgb(0,128,128)">$slice_adaptor</span><span style="font-weight:bold">-></span><span style="color:rgb(51,51,51)">fetch_by_stable_id</span><span>(</span><span style="color:rgb(0,128,128)">$Transcript</span><span>);</span></td>
</tr>
<tr>
<td style="padding:0px 10px;width:50px;min-width:50px;font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;font-size:12px;line-height:18px;color:rgba(0,0,0,0.298039);vertical-align:top;text-align:right;border-style:solid;border-color:rgb(238,238,238);border-width:0px 1px 0px 0px"><br>
</td>
<td style="padding:0px 10px;font-family:Consolas,'Liberation Mono',Menlo,Courier,monospace;font-size:12px;color:rgb(51,51,51);vertical-align:top;white-space:pre-wrap;overflow:visible">
<span style="font-weight:bold">my</span> <span style="color:rgb(0,128,128)">$translation</span>
<span style="font-weight:bold">=</span> <span style="color:rgb(0,128,128)">$tr</span><span style="font-weight:bold">-></span><span style="color:rgb(51,51,51)">translation</span><span>;</span></td>
</tr>
</tbody>
</table>
<br>
I suspect of <span style="color:rgb(0,128,128)">$config</span><span style="font-weight:bold">-></span><span>{</span><span style="color:rgb(51,51,51)">ga</span><span>} and </span><span style="color:rgb(0,128,128)">$config</span><span style="font-weight:bold">-></span><span>{</span><span style="color:rgb(51,51,51)">reg</span><span>} are the cause of this
problem, because I still see </span><span><span style="color:rgb(51,51,51)"><span style="color:rgb(51,51,51)">fetch_by_transcript_stable_id</span><span> and </span>fetch_by_stable_id</span><span></span> methods on
Ensembl API.<br>
<br>
Thanks !<br>
<br>
<br>
Best regards,<br>
Guillermo.<br>
</span>
</div>
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<br></blockquote></div><br></div>