Konstantin Riege | 4 Nov 17:02 2013

Bio::DB::SeqFeature::Store->features() problem

Hi,

I want to get all features by the primary_tag as shown in the 
documentation, but I get the error 'Argument "intron:" isn't numeric in 
numeric comparison (<=>) at /Bio/DB/SeqFeature/Store/berkeleydb3.pm line 
89.'
Is this a bug or did I any mistake?

use Bio::DB::SeqFeature::Store;
use Bio::SeqFeature::Generic;

my $db = Bio::DB::SeqFeature::Store->new( -adaptor => 'berkeleydb', -create 
=> 1 , -dsn => '/mnt/tmp/' );
$db->init_database([1]);
my  <at> features;
push  <at> features , Bio::SeqFeature::Generic->new(
-seq_id   =>   'BacSub.1',
-display_name => 'BacSub',
-start     =>   1,
-end        =>  10,
-strand => +1, 
-primary_tag  => 'exon',
-source     =>  'tool',
-score       => 60,
); 
push  <at> features , Bio::SeqFeature::Generic->new(
-seq_id   =>   'BacSub.2',
-display_name => 'BacSub',
-start     =>   11,
-end        =>  20,
-strand => +1, 
-primary_tag  => 'intron',
-source     =>  'tool',
-score       => 65,
);
$db->store( <at> features);

my  <at> foo = $db->features(-primary_tag  => 'intron');
print  <at> foo;

thanks

Gmane