[ensembl-dev] FuncGen - how to retrieve polII sites

[Daniel Zerbino]

Hello Marc,

You're warm... it's the AnnotatedFeatures you are looking for:

use strict;
use warnings;
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
     -host => 'ensembldb.ensembl.org',
     -user => 'anonymous'
     #The Registry automatically picks port 5306 for ensembl db
     #-verbose => 1, #specificy verbose to see exactly what it loaded
);

my $slice_adaptor = $registry->get_adaptor('Human', 'Core', 'Slice');
my $slice = $sa->fetch_by_region('chromosome', '1');

my $feature_type_adaptor = $registry->get_adaptor('Human', 'Core', 
'FeatureType');
my $feature_types = $feature_type_adaptor->fetch_all_by_name('PolIII');

my $feature_adaptor = $registry->get_adaptor('Human', 'Funcgen', 
'AnnotatedFeature');

foreach my $ft (@$feature_types) {
         my $features = $afa->fetch_all_by_Slice_FeatureType($slice, $ft);
         print scalar(@$features)."\n";
}



HTH,

Daniel

On 1/22/16 10:57 AM, Marc P. Hoeppner wrote:
> Hi,
>
> just started using the FuncGen API and was wondering how I can 
> retrieve Encode polII Sites for a given Slice. First issue is that I 
> am not sure which Adaptor these belong to, I guess. Tried 
> RegulatoryFeature and MotifFeature, but no luck. A quick pointer would 
> be greatly appreciated!
>
> Cheers,
> Marc
>
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