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Gmane
From: Konstantin Riege <koriege <at> googlemail.com>
Subject: Bio::DB::SeqFeature::Store->features() problem
Newsgroups: gmane.comp.lang.perl.bio.general
Date: Monday 4th November 2013 16:02:53 UTC (over 2 years ago)
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 @features;
push @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 @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(@features);

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

thanks
 
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