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