[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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