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

Joseph Guhlin guhli007 at umn.edu
Fri Jan 20 11:48:19 EST 2012


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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