[ensembl-dev] Support for storing structural variations / Ensembl registry bug for branch 66

[Jan Vogel]

Heya Ensembl,

I'm trying to import structural variations into a ensembl-variation database. 

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 : 

-------------------- EXCEPTION --------------------
MSG: Abstract method store not defined by implementing subclass

STACK Bio::EnsEMBL::DBSQL::BaseFeatureAdaptor::store …./ensembl/modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm:1105
STACK toplevel import_structual_variation_data.pl:65
Ensembl API version = 66
---------------------------------------------------

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 ?

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 ?


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:

cvs diff -r HEAD -r 1.220 Registry.pm
…..
<       'vega'          => 'Bio::EnsEMBL::DBSQL::DBAdaptor'
<       'vega_update'   => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
---
>       'vega'      => 'Bio::EnsEMBL::DBSQL::DBAdaptor',
>       'vega_update' => 'Bio::EnsEMBL::DBSQL::DBAdaptor',


Cheers, 

             Jan Vogel 



 

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