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

[Laurent Gil]

Hi Jan,

Actually we use the script you mentionned 
(/ensembl-variation/scripts/import/import_ega_sv_data.pl) to import 
directly DGVa data from GVF files (e.g. 
ftp://ftp.ebi.ac.uk/pub/databases/dgva/estd1_Redon_et_al_2006/gvf/).

I just implemented the method store in the HEAD code of the cvs:
- 
ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/BaseStructuralVariationAdaptor.pm
- 
ensembl-variation/modules/Bio/EnsEMBL/Variation/DBSQL/StructuralVariationFeatureAdaptor.pm
and a small fix in an other module (also in the HEAD code):
- ensembl-variation/modules/Bio/EnsEMBL/Variation/BaseStructuralVariation.pm

Please let me know if you still have some issues.

Cheers,

Laurent


On 20/03/2012 06:04, Jan Vogel 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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