[Bioperl-l] [Gmod-schema] beginning work on SeqIO::chadoxml

Scott Cain cain.cshl at gmail.com
Fri Feb 2 12:02:32 EST 2007


Ah, I'll go ahead and add one, though it will just throw an exception
because this is a write-only adapter.

Scott


On Fri, 2007-02-02 at 11:45 -0500, Hilmar Lapp wrote:
> There must be at least a stub for next_seq(). It may throw a not- 
> implemented exception, but it should not just be absent.
> 
> 	-hilmar
> 
> On Feb 2, 2007, at 11:37 AM, Chris Fields wrote:
> 
> > I was going to suggest maybe allowing one to switch out XML  
> > handlers/writers based on the style (ala XML::SAX), but I see that  
> > chadoxml currently uses XML::Writer and there is no next_seq()  
> > implemented.  Oh well...
> >
> > chris
> >
> > On Feb 2, 2007, at 10:03 AM, Scott Cain wrote:
> >
> >> Hi Hilmar,
> >>
> >> That is a good idea; when I started down this road, it felt like  
> >> there
> >> would only be a few things that I might want to allow to be  
> >> different,
> >> but I think you are right that having one standard implementation  
> >> that
> >> can be subclassed for legacy systems is a good thing.
> >>
> >> Scott
> >>
> >>
> >> On Fri, 2007-02-02 at 10:09 -0500, Hilmar Lapp wrote:
> >>> On Feb 1, 2007, at 2:55 PM, Scott Cain wrote:
> >>>
> >>>> The second main change was to introduce a -flybase_compat argument
> >>>> when
> >>>> initializing the Bio::SeqIO writer, so that 'old style' cv and  
> >>>> cvterms
> >>>> (that are compatable with flybase) will be used, but now the  
> >>>> default
> >>>> will be to use current standards:
> >>>
> >>> Just my $0.02 ... obviously, Flybase may be the only organization
> >>> that uses an 'old style' or any other way not compliant with  
> >>> 'current
> >>> standards' (presumably SO), but if it's not the only one then this
> >>> approach won't scale.
> >>>
> >>> Also, an argument -flybase_compat suggests to the unsuspecting that
> >>> this is an endorsed flavor of the standard and fine to use for
> >>> everyone else too.
> >>>
> >>> If Flybase is idiosyncratic in this way, why not make chadoxml.pm
> >>> compliant with the standard as we all want it, keep it free from
> >>> litter caused by usage of old versions of SO, and create a second
> >>> module fb-chadoxml.pm that inherits from the first and merely
> >>> overrides a few things so that it works for Flybase. This way, other
> >>> organizations with similar needs can follow the path and create  
> >>> their
> >>> own xyz-chadoxml.pm, rather than having to muck around in the
> >>> chadoxml.pm that comes with the distribution.
> >>>
> >>> I'm not sure I fully grasp the underlying issue, so I may not make
> >>> much sense here. Apologies if that's the case ...
> >>>
> >>> 	-hilmar
> >> -- 
> >> --------------------------------------------------------------------- 
> >> ---
> >> Scott Cain, Ph. D.                                    
> >> cain.cshl at gmail.com
> >> 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

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