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

[Andy Yates]

Hi Jan,

Thanks for flagging up the issue in the registry. Looks like a change which only went in a few hours ago. We'll have it backed out of CVS soon.

Cheers

Andy

On 20 Mar 2012, at 06:04, Jan Vogel <jan.vogel at gmail.com> wrote:

> 
> 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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