[Bioperl-l] Problem with Bio::Annotation

[Hilmar Lapp]

You need to pass an implementation of Bio::AnnotationCollectionI. Bio::Annotation::Collection is the reference implementation - it will most likely suffice for what you want.

(BTW since 1.1.1 what you do will throw an exception to better tell people that the API has changed.)

	-hilmar

> -----Original Message-----
> From: Harry Wild [mailto:harry.wild@gmx.de]
> Sent: Tuesday, December 10, 2002 7:02 AM
> To: bioperl-l@bioperl.org
> Subject: [Bioperl-l] Problem with Bio::Annotation
> 
> 
> 
> Hi bioperl Community!
> 
> I'm trying to write out genome data from a relational 
> database to Genbank
> format. 
> But I'm not able to get the annotations out of the Seq-Objects that I
> create.
> 
> My little test-code
> 
> 	use Bio::SeqIO;
> 	use Bio::Seq;
> 	use Bio::Annotation;
> 
> 	$out = Bio::SeqIO->new( -file => ">/home/wild/test1.gb" ,
>                        	                      -format 
> => 'GenBank');
> 
> 	$seq = Bio::Seq->new( '-seq' => 'atgcctgatctggatcgtt',
>                                              '-display_id' => 
> 'something',
>                                              '-accession_number' =>
> 'AC_000001');
> 
> 	$seq->annotation( new Bio::Annotation( '-description' => 'some
> description'));
> 
> 	$out->write_seq($seq);
> 
> 	$out->close;
> 
> always produces the following output:
> 
> Can't locate object method "get_Annotations" via package 
> "Bio::Annotation"
> at 
> /usr/local/lib/perl5/site_perl/5.005/Bio/SeqIO/genbank.pm line 466.
> 
> What's wrong with my code?
> 
> Thanks for help,
> Harry
> 
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