[Bioperl-l] Error writing out EMBL

michael watson (IAH-C) michael.watson at bbsrc.ac.uk
Wed May 4 08:33:59 EDT 2005


Hi

I'm on bioperl-1.5.

I get this when writing out an EMBL file:

FT
/gene_id="Bio::Annotation::SimpleValue=HASH(0x858d688)"
FT
/note="Bio::Annotation::SimpleValue=HASH(0x8595360)"

My code is:

use Bio::Perl;
use Bio::SeqIO;
use Bio::Seq;
use Bio::SeqFeature::Generic;

my $seq = Bio::Seq->new(-display_id => 'test',
			-seq => "ACGTACGTACGTACGT");

my $gene = "test gene";

my $gene_feat = Bio::SeqFeature::Generic->new(-start   => 2, 
					      -end     => 5,
					      -primary => 'CDS',
					      -tag => {gene_id => $gene,
						       note => 'test
gene'});

$seq->add_SeqFeature($gene_feat);  

write_sequence(">test.embl",'embl',$seq);  


Why are my gene_id and note tags being written as bioperl object
references?  This didn't happen in 1.4! :-)

Many thanks
Mick



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