<div dir="ltr">Hi Phil,<div><br></div><div style>The adaptor you create in your registry needs to be under the Variation sub-class:</div><div style><br></div><div style><span style="font-family:arial,sans-serif;font-size:13px">new Bio::EnsEMBL::Variation::DBSQL::</span><span style="font-family:arial,sans-serif;font-size:13px">DBAdaptor(</span><br>
</div><div style><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div style><span style="font-family:arial,sans-serif;font-size:13px">instead of</span></div><div style><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div><div style><span style="font-family:arial,sans-serif;font-size:13px">new Bio::EnsEMBL::DBSQL::</span><span style="font-family:arial,sans-serif;font-size:13px">DBAdaptor(</span><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div><div style><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div style><span style="font-family:arial,sans-serif;font-size:13px">Regards</span></div><div style><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div><div style><span style="font-family:arial,sans-serif;font-size:13px">Will McLaren</span></div><div style><span style="font-family:arial,sans-serif;font-size:13px">Ensembl Variation</span></div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On 5 March 2013 20:59, Phil Dagosto <span dir="ltr"><<a href="mailto:PDagosto@edgebio.com" target="_blank">PDagosto@edgebio.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-US" link="blue" vlink="purple">
<div>
<p class="MsoNormal">I'm trying to import a VCF file into my local Ensembl variation database.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">The version of the API I'm using is 70.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Here are the contents of my registry file:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">use Bio::EnsEMBL::Utils::ConfigRegistry;<u></u><u></u></p>
<p class="MsoNormal">use Bio::EnsEMBL::DBSQL::DBAdaptor;<u></u><u></u></p>
<p class="MsoNormal">use Bio::EnsEMBL::Variation::DBSQL::DBAdaptor;<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">new Bio::EnsEMBL::DBSQL::DBAdaptor(<u></u><u></u></p>
<p class="MsoNormal"> -host => 'local_ensembl',<u></u><u></u></p>
<p class="MsoNormal"> -user => 'test',<u></u><u></u></p>
<p class="MsoNormal"> -pass => '123', <u></u>
<u></u></p>
<p class="MsoNormal"> -port => '3306',<u></u><u></u></p>
<p class="MsoNormal"> -species => 'Homo sapiens',<u></u><u></u></p>
<p class="MsoNormal"> -group => 'variation',<u></u><u></u></p>
<p class="MsoNormal"> -dbname => 'homo_sapiens_variation_70_37'<u></u><u></u></p>
<p class="MsoNormal">);<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">my @aliases = ( 'H_Sapiens', 'human' );<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(<u></u><u></u></p>
<p class="MsoNormal"> -species => 'Homo sapiens',<u></u><u></u></p>
<p class="MsoNormal"> -alias => \@aliases<u></u><u></u></p>
<p class="MsoNormal">);<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">1;<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">The import_vcf .pl script is being run with the following command-line parameters:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">--input_file indel.final.vcf --registry <a href="http://registry.pl" target="_blank">registry.pl</a> --source 'edgebio' --population 'test' --test 100<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">The output is:<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">2013-03-05 15:54:33 - Session ID is 64494fac5e75b495bfb5907137f45cbf<u></u><u></u></p>
<p class="MsoNormal">2013-03-05 15:54:40 - Connected to database homo_sapiens_variation_70_37 on local_ensembl as user test<u></u><u></u></p>
<p class="MsoNormal">ERROR: Could not get population adaptor<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Is there something I need to add to my Registry file so that the population adaptor can be found?<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks,<span class="HOEnZb"><font color="#888888"><u></u><u></u></font></span></p><span class="HOEnZb"><font color="#888888">
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Phil<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
</font></span></div>
</div>
<br>_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><br>
<br></blockquote></div><br></div>