<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><br></div><div>Heya Ensembl,</div><div><br></div><div>I'm trying to import structural variations into a ensembl-variation database. </div><div><br></div><div>Currently I am creating a few Bio::EnsEMBL::Variation::StructuralVariationFeature() objects and than add them to the Bio::EnsEMBL::Variation::DBSQL::StructuralVariationFeatureAdaptor - i tried to call the store() method but get an exception : </div><div><br></div><div><div><font class="Apple-style-span" face="Courier">-------------------- EXCEPTION --------------------</font></div><div><font class="Apple-style-span" face="Courier">MSG: Abstract method store not defined by implementing subclass</font></div><div><font class="Apple-style-span" face="Courier"><br></font></div><div><font class="Apple-style-span" face="Courier">STACK Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::store …./ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm:1105</font></div><div><font class="Apple-style-span" face="Courier">STACK toplevel import_structual_variation_data.pl:65</font></div><div><font class="Apple-style-span" face="Courier">Ensembl API version = 66</font></div><div><font class="Apple-style-span" face="Courier">---------------------------------------------------</font></div></div><div><br></div><div>It seems that there's currently no API support to store structural variations in an ensembl variation database. So, how do these features get imported from DGVa into Ensembl ?</div><div><br></div><div>I came across a script : /ensembl-variation/scripts/import/import_ega_sv_data.pl which has a lot of raw sql in it - are you using this script ?</div><div><br></div><div><br></div><div>Ah, btw there's a bug in Bio::EnsEMBL::Registry for branch-ensembl-66 -: the "end-comma" is missing in line 169 - it's fixed in the trunk:</div><div><br></div><div><font class="Apple-style-span" face="Courier">cvs diff -r HEAD -r 1.220 Registry.pm</font></div><div>…..</div><div><span class="Apple-style-span" style="font-family: Courier; ">< 'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor'</span><font class="Apple-style-span" face="Courier"><div>< 'vega_update' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',</div><div>---</div></font><span class="Apple-style-span" style="font-family: Courier; ">> 'vega' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',</span><font class="Apple-style-span" face="Courier"><div>> 'vega_update' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',</div><div><br></div></font></div><div><br></div><div>Cheers, </div><div><br></div><div> Jan Vogel </div><div><br></div><div><br></div><div><br></div><div> </div><div><br></div></body></html>