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

[Nathan Johnson]

We added gender support at the start of last year, for v60 I think.

I'm not sure you are using the v53 API.  As I have just rerun a snippet from you code using v53 and it gives a different error, as the fetch_all_by_feature_class method was added after v53 (v59 I think).

To find out add '-verbose => 1', to your registry load method. This will list the DBs being loaded, which should match your API version, if you have not over-ridden it.


wrt the biomart query. The link doesn't work for me. Can you copy and paste the filter and attributes from the left hand panel?

I suspect you are trying to select filters from more than one 'Feature' section, which will (at present) always return no data. This is because the mart filters use 'AND' logic e.g.
	'RegulatoryFeature filter' AND 'AnnotatedFeature filter'. 

As any one result cannot be both a RegulatoryFeature and an AnnotatedFeature, there will be no results.  We have put in a request to change this with the Biomart developers, so hopefully we can make this a little easier to use in future.

Nath


On 8 Apr 2011, at 13:48, Fiona Nielsen wrote:

> Hi Nathan,
> 
> My API version is not up-to-date:
> The example was run using the Ensembl 53 API and the DB at ensembldb.ensembl.org
> I will try to run it again after updating all the API packages.
> 
> Can you see from what version these functions are available?
> 
> and do you have an explanation for the missing data in BioMart?
> http://www.ensembl.org/biomart/martview/e809b93c2b06f0bca4dfda066952fa56/e809b93c2b06f0bca4dfda066952fa56?VIRTUALSCHEMANAME=default&ATTRIBUTES=hsapiens_feature_set.default.annotated_feature.fs_display_label_1048|hsapiens_feature_set.default.annotated_feature.feature_type_name_1048|hsapiens_feature_set.default.annotated_feature.seq_region_name_1048|hsapiens_feature_set.default.annotated_feature.seq_region_start_1048|hsapiens_feature_set.default.annotated_feature.seq_region_end_1048|hsapiens_feature_set.default.annotated_feature.cell_type_name_1048|hsapiens_feature_set.default.annotated_feature.feature_type_class_1048|hsapiens_feature_set.default.annotated_feature.feature_type_description_1048|hsapiens_feature_set.default.annotated_feature.cell_type_display_label_1048|hsapiens_feature_set.default.annotated_feature.cell_type_description_1048&FILTERS=&VISIBLEPANEL=resultspanel
> 
> 
> Thanks,
> 
> -Fiona-
> 
> On Fri, Apr 8, 2011 at 2:32 PM, Nathan Johnson <njohnson at ebi.ac.uk> wrote:
>> 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-
>>> 
>>> _______________________________________________
>>> Dev mailing list
>>> Dev at ensembl.org
>>> http://lists.ensembl.org/mailman/listinfo/dev
>> 
>> Nathan Johnson
>> Senior Scientific Programmer
>> Ensembl Regulation
>> European Bioinformatics Institute
>> Wellcome Trust Genome Campus
>> Hinxton
>> Cambridge CB10 1SD
>> 
>> http://www.ensembl.info/
>> http://twitter.com/#!/ensembl
>> 
>> 
>> 
>> 
>> 
>> 
>> 

Nathan Johnson
Senior Scientific Programmer
Ensembl Regulation
European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD

http://www.ensembl.info/
http://twitter.com/#!/ensembl