[Bioperl-l] Bio::DB::SeqFeature::Store->features() problem
Konstantin Riege
koriege at googlemail.com
Mon Nov 4 11:02:53 EST 2013
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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