[Bioperl-l] Feature/Annotation rollback finished

Scott Cain cain.cshl at gmail.com
Thu Aug 30 11:46:24 EDT 2007


Hi Chris,

Good news!  I only had to add a few defineds and a few display_texts and
I was able to successfully create a database and load the yeast GFF3
file.  While I want to do more testing with GFF from other sources,
clearly, I am 95% of the way there with relatively little work.

Nice job and Thanks!
Scott


On Wed, 2007-08-29 at 23:17 -0500, Chris Fields wrote:
> It shouldn't, that sounds like the output for add_text().  value()  
> should just return the scalar value.
> 
> As a note, I added a new method, display_text(), for all  
> Bio::AnnotationI classes which by default replicates the same output  
> that stringification overloads produced.  So you should be able to  
> explicitly call $ann->display_text for any Bio::AnnotationI where you  
> once used an implicit call:
> 
> # old
> print "$ann\n";
> 
> # new
> print $ann->display_text,"\n";
> 
> chris
> 
> On Aug 29, 2007, at 11:05 PM, Scott Cain wrote:
> 
> > Hi Chris,
> >
> > Is there a reason that the value method of the
> > Bio::Annotation::SimpleValue (and possibly some of its siblings)
> > returning "Value: $value"?  It didn't used to have the "Value: "  
> > before,
> > did it?
> >
> > Thanks,
> > Scott
> >
> >
> > On Wed, 2007-08-29 at 15:13 -0500, Chris Fields wrote:
> >> I'll probably go ahead and start merging this stuff over to CVS HEAD
> >> then.  There haven't been any objections so far.
> >>
> >> The page I posted outlines the more critical fixes, primarily the
> >> changes to Bio::Ontology::Term methods (along with relevant code) due
> >> to inconsistencies in the interface.  The Bio::Annotation classes
> >> also now throw if you attempt to use them in an overloaded context.
> >> I also split off SeqFeature::Annotated tests into it's own test suite
> >> (SeqFeatAnnotated.t).
> >>
> >> Let me know if there are any problems along the way!
> >>
> >> chris
> >>
> >> On Aug 29, 2007, at 2:45 PM, Scott Cain wrote:
> >>
> >>> Hi Chris,
> >>>
> >>> I just wanted to let you know that I was out of town for a few
> >>> days, but
> >>> now I'm back and I'm doing testing of GMOD software based on the
> >>> branch
> >>> you are working on.  I'll let you know how it goes, but don't let me
> >>> stop you if you confident of your changes.  I'm sure whatever goes
> >>> wrong, it will just point out holes in the FeatureIO tests (I'm sure
> >>> there are plenty) and will require hopefully minimal changes on my
> >>> end.
> >>>
> >>> Thanks for your considerable efforts on this!  (Regardless of how  
> >>> much
> >>> work it makes for me :-)
> >>> Scott
> >>>
> >>>
> >>> On Tue, 2007-08-28 at 16:05 -0500, Chris Fields wrote:
> >>>> I'm now wrapping up the Feature/Annotation rollback.  I will  
> >>>> probably
> >>>> start merging back to the main branch in the next day or two., as
> >>>> soon as interested parties (*cough*devs*cough*) look over the last
> >>>> batch of changes.
> >>>>
> >>>> http://www.bioperl.org/wiki/ 
> >>>> Feature_Annotation_rollback#Fourth_Round
> >>>>
> >>>> I have also added a small benchmark test which indicates a decrease
> >>>> in parsing time in SeqIO::genbank with all tests passing.  I expect
> >>>> this will translate over to any Bio::SeqFeature::Generic-using  
> >>>> class
> >>>> (open mouth, prepare to insert foot....).
> >>>>
> >>>> It is also possible there are still some instances where  
> >>>> overloading
> >>>> is expected lurking about in the ~1000 or so modules, so I'll leave
> >>>> the exceptions I added to all Bio::AnnotationI; we can remove them
> >>>> down the line, maybe prior to rel1.6, after more tests are added or
> >>>> if they get particularly annoying.  My guess is I caught 99.99% of
> >>>> them (prepare to insert other foot....).
> >>>>
> >>>> The key change in this last round is the addition of several class
> >>>> *dbxref* methods to Bio::Ontology::Term and
> >>>> Bio::Annotation::OntologyTerm, all of which are capable of working
> >>>> with either DBLink instances or simple scalars.  This was primarily
> >>>> done in order to clear up inconsistencies in the older *dblink*
> >>>> methods, which were ambiguous (some indicates simple scalar
> >>>> arguments, others DBLink objects); operator overloading was used
> >>>> extensively in these cases, which led to several issues.  I have
> >>>> added deprecation warnings to the older methods which now map to
> >>>> using the newer methods.  All tests pass with the exception of a  
> >>>> few
> >>>> already failing on the MAIN branch; the single test which needs  
> >>>> to be
> >>>> fixed is a round-tripping error in swiss.t (now a TODO), which  
> >>>> can be
> >>>> fixed after merging back.
> >>>>
> >>>> Please respond to this if there are any questions or if I need to
> >>>> clarify the changes I made a bit more.
> >>>>
> >>>> chris
> >>>> _______________________________________________
> >>>> Bioperl-l mailing list
> >>>> Bioperl-l at lists.open-bio.org
> >>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>> -- 
> >>> -------------------------------------------------------------------- 
> >>> --
> >>> --
> >>> Scott Cain, Ph. D.
> >>> cain at cshl.edu
> >>> GMOD Coordinator (http://www.gmod.org/)
> >>> 216-392-3087
> >>> Cold Spring Harbor Laboratory
> >>> _______________________________________________
> >>> Bioperl-l mailing list
> >>> Bioperl-l at lists.open-bio.org
> >>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >>
> >> Christopher Fields
> >> Postdoctoral Researcher
> >> Lab of Dr. Robert Switzer
> >> Dept of Biochemistry
> >> University of Illinois Urbana-Champaign
> >>
> >>
> >>
> > -- 
> > ---------------------------------------------------------------------- 
> > --
> > Scott Cain, Ph. D.                                    
> > cain.cshl at gmail.com
> > GMOD Coordinator (http://www.gmod.org/)                      
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> >
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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