[Bioperl-l] Strange Error, Bio::Graphics::Feature attach_seq is not implemented

Scott Cain scott at scottcain.net
Fri Jan 20 12:29:07 EST 2012


Hi Joseph,

I agree that Bio::Graphics::Feature doesn't have an attach_seq method,
nor does Bio::SeqFeature::Lite that it inherits from.  I don't know
why they don't--it might be a design decision, or it could just be an
oversight.  In the mean time, is there a reason you couldn't use
Bio::SeqFeature::Generic?  The only place in the Bio::Graphics or
GBrowse code base that the attach_seq method is used is in
Bio::Graphics::Glyph::dna, and it uses a Bio::SeqFeature::Generic.

Scott


On Fri, Jan 20, 2012 at 11:48 AM, Joseph Guhlin <guhli007 at umn.edu> wrote:
> Is this the right place to send it? I couldn't find anything in the
> archives. I've got a simple plugin I'm working on for gbrowse, and have
> been having trouble. I removed it from gbrowse completely, and am running
> the script. I get this error:
>
> ------------- EXCEPTION: Bio::Root::NotImplemented -------------
> MSG: Abstract method "Bio::SeqFeatureI::attach_seq" is not implemented by
> package Bio::Graphics::Feature.
> This is not your fault - author of Bio::Graphics::Feature should be blamed!
>
> STACK Bio::Root::RootI::throw_not_implemented
> /opt/local/lib/perl5/site_perl/5.12.3/Bio/Root/RootI.pm:748
> STACK Bio::SeqFeatureI::attach_seq
> /opt/local/lib/perl5/site_perl/5.12.3/Bio/SeqFeatureI.pm:289
> STACK toplevel dnaglyphtest.pl:45
> ----------------------------------------------------------------
>
> I made use Bio::Graphics and BioPerl were up to date with CPAN. It works if
> I use it as a Bio::SeqFeature::Generic but all the references I've found
> says you can use it as a feature. Putting in a workaround here but not
> familiar enough with BioPerl to make a patch.
>
> Could it be something I'm missing as well?
>
> This is testing code to find where the problem is, ignore how terrible it
> looks and how redundant most of it is. It's just me ripping it out to get
> to the error(GBrowse doesn't seem to like to give out error messages, but
> that's unrelated...)
>
> http://pastebin.ca/2104560
>
>
>
> Thanks,
> --Joseph
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research



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