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

Joseph Guhlin guhli007 at umn.edu
Fri Jan 20 13:41:15 EST 2012


Thanks for the offer. I think since I am going to be re-working the dna
glyph for my purposes I'm just going to use a simple work around for now. I
do appreciate the offer of help though. If I revisit it in the future I'll
try to look at it, it could easily be a crash due to my own newness to the
bioperl/gbrowse system.

Best,
--Joseph

On Fri, Jan 20, 2012 at 12:28 PM, Scott Cain <scott at scottcain.net> wrote:

> Hi Joseph,
>
> I'm guessing Bio::SeqFeature::Lite could be modified fairly easily to
> add an attach_seq method; unfortunately I don't have the time to do
> that today.
>
> Perhaps we should look at the nature of the crash when you're using
> Bio::SeqFeature::Generic; maybe that will be easier to solve.
>
> Scott
>
>
> On Fri, Jan 20, 2012 at 12:51 PM, Joseph Guhlin <guhli007 at umn.edu> wrote:
> > 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
> >
> >
>
>
>
> --
> ------------------------------------------------------------------------
> 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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