[Bioperl-l] Error writing out EMBL

[Hilmar Lapp]

This is a known problem. Use 1.4 instead, or use the CVS downloads from 
either the 1.4 branch or the main trunk.

	-hilmar

On Wednesday, May 4, 2005, at 05:33  AM, michael watson ((IAH-C)) wrote:

> 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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>
>
-- 
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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