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

Scott Cain scott at scottcain.net
Fri Jan 20 13:28:12 EST 2012


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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