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

Fields, Christopher J cjfields at illinois.edu
Fri Jan 20 15:02:06 EST 2012


Scott,

I think the problem is that the original attach_seq() interface method (and Bio::SF::Generic) assumed an in-memory generic Bio::Seq/PrimarySeq, but the design for Bio::SF::Lite and Bio::Graphics::Feature I believe assumed such data are not stored as an in-memory Bio::SeqI, but in a database or a file.

It's possible to implement this for the basic non-persistent cases mentioned but override the method, initially as unimplemented, in child classes where a different behavior is expected (Bio::DB::SeqFeature for example).

(Hope that makes sense?)

chris

On Jan 20, 2012, at 12:28 PM, Scott Cain 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
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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