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

Joseph Guhlin guhli007 at umn.edu
Fri Jan 20 12:51:36 EST 2012


Hi, thanks for the response.

I'm trying to create a plugin that uses the dna glyph(which says you can
use a B::G::Feature in its POD) and then I'm going to expand upon it. I'm
guessing it is an oversight and have implemented them in another object for
now and just inheriting that class.

I'm still new to gbrowse2 but when I tried to attach a
Bio::SeqFeature::Generic object to a featurelist it would crash at that
point, so I went back to using the Bio::Graphics::Feature objects and it
worked again(using other glyphs, experimenting around and learning). This
might be off topic but any ideas around?

I wanted to see if I did something weird that was causing it to
die(something not installed, misconfigured).

Best,
--Joseph

On Fri, Jan 20, 2012 at 11:29 AM, Scott Cain <scott at scottcain.net> wrote:

> 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
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>
>
>
> --
> ------------------------------------------------------------------------
> 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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