[Bioperl-l] ->add_tag_value()

[Jason Stajich]

It has been discussed several times on the mailing list.  A  
deficiency in the code released as 1.5.0 but should be fixed in CVS  
now.  If it isn't can you please yell loudly so it gets fixed by the  
people who broke it... =)

  http://portal.open-bio.org/pipermail/bioperl-l/2005-April/018749.html

-jason
On Aug 25, 2005, at 5:08 PM, Andrew Stewart wrote:

> I'm trying to create genbank files from a sequence file and  
> features retreived from glimmer output.  When creating the new  
> features and writing them to the genbank (richseq) object, though,  
> I get the following output (for example)...
>
>     CDS             21..596
>                     /translation="Bio::Annotation::SimpleValue=HASH 
> (0x987b78)"
>     CDS             complement(1713..2903)
>                     /translation="Bio::Annotation::SimpleValue=HASH 
> (0x987944)"
>     CDS             complement(3236..4258)
>                     /translation="Bio::Annotation::SimpleValue=HASH 
> (0x9be8e4)"
>     CDS             4350..5936
>                     /translation="Bio::Annotation::SimpleValue=HASH 
> (0x9bead0)"
>     CDS             6181..6819
>                     /translation="Bio::Annotation::SimpleValue=HASH 
> (0x9bebd8)"
>
> The translation tag I added is for some reason being shown as a  
> hash.  The code in question is here...
>
>    my $translation = $seqo->subseq($start, $stop);
>    $feat->add_tag_value("translation",$translation);
>
> Everything there is ok, as far as I can tell.  I was able to spit  
> the 'translation' tag back out with some test code just fine.  Near  
> as I can tell, either $feat->add_tag_value() is setting the tag  
> value as a reference, or the tag value is being retreived as such  
> when the feature is written to the seq object (or somewhere else in  
> the process).
>
> Anyone have any idea what might be going on here?
>
>
> -Andrew Stewart
> BDRD
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/