[ensembl-dev] error retrieving annotated features from Ensembl Regulation 61

[Nathan Johnson]

Hello Fiona

I have tested this and can't recreate the error.  I suspect this maybe an API version issue, as the gender attribute was added in the last 12 months I think.

What version API and DBs are you using?

Thanks

Nath


On 8 Apr 2011, at 12:47, Fiona Nielsen wrote:

> I am trying to extract Ensembl data related to the annotated features
> in the Ensembl Regulation database.
> 
> The function to access regulatory features is executed with no error:
> 
>    # set database adaptor
>    my $efg_db       = $registry->get_DBAdaptor('Human', 'funcgen');
> 
>    # retrieve feature set from database
>    my $fset_adaptor = $registry->get_adaptor('Human','funcgen','featureset');
> 
>    # retrieve all regulatory FeatureSets
>    # 'annotated', 'regulatory' or 'supporting'
>    my @rf_fsets = @{$fset_adaptor->fetch_all_by_feature_class('regulatory')};
> 
>    foreach my $rf_fset(@rf_fsets){
> 	print $rf_fset->name.",";
>    }
> 
> but when trying to access the annotated features, I get an error message
>    # set database adaptor
>    my $efg_db       = $registry->get_DBAdaptor('Human', 'funcgen');
> 
>    # retrieve feature set from database
>    my $fset_adaptor = $registry->get_adaptor('Human','funcgen','featureset');
> 
>    # retrieve all regulatory FeatureSets
>    # 'annotated', 'regulatory' or 'supporting'
>    my @rf_fsets = @{$fset_adaptor->fetch_all_by_feature_class('annotated')};
> 
> DBD::mysql::st execute failed: Unknown column 'ct.gender' in 'field
> list' at ../ensembl/modules//Bio/EnsEMBL/DBSQL/BaseAdaptor.pm line
> 477.
> 
> 
> I tried to have a look in BioMart, and if I in BioMart select "Homo
> Sapiens features" and "annotated features", I am only served empty
> rows in the result.
> Are these data sets not available or is there some bug in the API to
> retrieve them?
> 
> Any comments and suggestions are welcome.
> 
> Thanks,
> 
> -Fiona-
> 
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Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

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