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<p>Hi Guillermo,</p>
<p>We need look into it to highlight/fix the compatibility issues of
the VEP plugins with the new VEP.<br>
</p>
<p>In the meantime, you can define your own Gene adaptor in your
self coded plugins, by inserting this code in each plugin (sorry):</p>
<span class="sh_keyword">use</span> Bio<span class="sh_symbol">::</span>EnsEMBL<span
class="sh_symbol">::</span>Registry<span class="sh_symbol">;</span>
<span class="sh_keyword"><br>
<br>
my</span> <span class="sh_variable">$registry</span> <span
class="sh_symbol">=</span> <span class="sh_string">'Bio::EnsEMBL::Registry'</span><span
class="sh_symbol">;</span><br>
<span class="sh_variable">$registry</span><span class="sh_symbol">-></span><span
class="sh_function">load_registry_from_db</span><span
class="sh_symbol">(</span><br>
<span class="sh_symbol">-</span>host <span class="sh_symbol">=></span>
<span class="sh_string">'ensembldb.ensembl.org'</span><span
class="sh_symbol">,</span> <span class="sh_comment">#
alternatively 'useastdb.ensembl.org'<br>
</span> <span class="sh_symbol">-</span>user <span
class="sh_symbol">=></span> <span class="sh_string">'anonymous'</span><span
class="sh_symbol"><br>
);</span><br>
my $gene_adaptor = <span class="sh_variable">$registry</span><span
class="sh_symbol">-></span><span class="sh_function">get_adaptor</span><span
class="sh_symbol">(</span> <span class="sh_string">'Human'</span><span
class="sh_symbol">,</span> <span class="sh_string">'Core'</span><span
class="sh_symbol">,</span> <span class="sh_string">'Gene'</span>
<span class="sh_symbol">); # e.g. if you work on human data<br>
<br>
</span><span class="pl-smi">$self</span><span class="pl-k">-></span>{<span
class="pl-c1">ga</span>} = $gene_adaptor; # If you want to keep
using the variable <span class="pl-smi">$self</span><span
class="pl-k">-></span>{<span class="pl-c1">ga</span>}.<br>
<span class="pl-smi"></span><span class="pl-k"></span><span
class="pl-c1"></span><br>
You can have further explanations about this code in the Ensembl API
tutorial:
<a class="moz-txt-link-freetext" href="http://www.ensembl.org/info/docs/api/core/core_tutorial.html">http://www.ensembl.org/info/docs/api/core/core_tutorial.html</a><br>
<br>
I hope this will solve your issue.<br>
Best regards,<br>
<pre class="moz-signature" cols="72">Laurent
Ensembl Variation
</pre>
<div class="moz-cite-prefix">On 15/05/2017 12:06, Guillermo Marco
Puche wrote:<br>
</div>
<blockquote type="cite"
cite="mid:0cf9f321-37a9-97d8-752a-bd48618e0602@sistemasgenomicos.com">
<meta content="text/html; charset=utf-8" http-equiv="Content-Type">
<p>Hi Laurent,</p>
<p>Thank you for your quick answer. I'm using gene adaptor in some
self coded plugins too. Do you have any quick-fix in mind or
workaround?<br>
I'm really looking forward for this document. Will it be
announced in mailing list or blog? I was really scared with this
big VEP update for the plugin compatibility. <br>
</p>
<p>Best regards,<br>
Guillermo.<br>
</p>
<br>
<div class="moz-cite-prefix">On 05/15/2017 12:17 PM, Laurent Gil
wrote:<br>
</div>
<blockquote
cite="mid:2f11bc77-1156-1abd-c49a-cad5ea062903@ebi.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=utf-8">
<p>Hi Guillermo,</p>
<p>Unfortunately the VEP plugin is not compatible with the new
ensembl-vep repository.<br>
We need to document this plugin about this compatibility
issue.<br>
</p>
However the new VEP (ensembl-vep) has a new option '-nearest
gene' you can use with the cache:<br>
<a moz-do-not-send="true"
href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#output">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#output</a><br>
<p>Best regards,<i><br>
</i></p>
<pre class="moz-signature" cols="72">Laurent</pre>
<div class="moz-cite-prefix">On 15/05/2017 08:44, Guillermo
Marco Puche wrote:<br>
</div>
<blockquote type="cite"
cite="mid:2dbb3ab7-01ba-2322-2f54-b481aa377eb0@sistemasgenomicos.com">
<meta http-equiv="content-type" content="text/html;
charset=utf-8">
<p>Dear devs,</p>
<p>I've recently updated to Ensembl VEP 88 and I'm facing some
problems with some plugins. Trying to run NearestGene.pm
plugin and I can't make it run.</p>
<p><i>WARNING: Plugin 'NearestGene' went wrong: ERROR: Could
not get gene adaptor; this plugin does not work in
--offline mode</i></p>
<p>There's an issue with gene adaptor code,<b> $self->{ga}
||= $self->{config}->{ga}</b>. Trying to guess where
did {ga} gone printing Dump of $self->{config} but I
can't figure this out:</p>
<p>$VAR1 = {<br>
'buffer_size' => 5000,<br>
'af_1kg' => 1,<br>
'species' => 'homo_sapiens',<br>
'stats_html' => 1,<br>
'host' => 'sake',<br>
'format' => 'vcf',<br>
'reg' => 'Bio::EnsEMBL::Registry',<br>
'chunk_size' => 50000,<br>
'check_existing' => 1,<br>
'freq_pop' => '1KG_ALL',<br>
'custom' => [],<br>
'cell_type' => [],<br>
'input_file' => 'test.vcf',<br>
'tmpdir' => '/tmp',<br>
'freq_filter' => 'exclude',<br>
'user' => 'bioinfo',<br>
'phastCons' => [],<br>
'terms' => 'SO',<br>
'delimiter' => ' ',<br>
'dir_cache' => '/home/gmarco/.vep',<br>
'polyphen_analysis' => 'humvar',<br>
'cache' => 1,<br>
'port' => '3306',<br>
'plugin' => [<br>
'Test'<br>
],<br>
'freq_gt_lt' => 'gt',<br>
'output_format' => 'vcf',<br>
'phyloP' => [],<br>
'numbers' => 1,<br>
'af_exac' => 1,<br>
'output_file' => '/tmp/test_88.vcf',<br>
'database' => 0,<br>
'freq_freq' => '0.01',<br>
'dir_plugins' =>
'/home/gmarco/repositories/vep_ensembl/Plugins',<br>
'core_type' => 'core',<br>
'vcf' => 1,<br>
'assembly' => 'GRCh38',<br>
'af' => 1,<br>
'terminal_width' => 48,<br>
'vcf_info_field' => 'CSQ',<br>
'transcript_filter' => [],<br>
'af_esp' => 1,<br>
'pick_order' => [<br>
'canonical',<br>
'appris',<br>
'tsl',<br>
'biotype',<br>
'ccds',<br>
'rank',<br>
'length',<br>
'ensembl',<br>
'refseq'<br>
],<br>
'biotype' => 1,<br>
'cache_region_size' => 1000000,<br>
'symbol' => 1,<br>
'ucsc_data_root' => '<a class="moz-txt-link-freetext"
href="http://hgdownload.cse.ucsc.edu/goldenpath/"
moz-do-not-send="true">http://hgdownload.cse.ucsc.edu/goldenpath/</a>',<br>
'synonyms' =>
'/home/gmarco/.vep/homo_sapiens/88_GRCh38/chr_synonyms.txt',<br>
'dir' => '/home/gmarco/.vep',<br>
'password' => 'A29bcd1234#',<br>
'no_slice_cache' => 1,<br>
'failed' => 0,<br>
'force_overwrite' => 1,<br>
'fasta' =>
'/home/gmarco/.vep/homo_sapiens/88_GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.gz'<br>
};</p>
<p>Regards,<br>
Guillermo<br>
</p>
<p><br>
<br>
</p>
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