[Bioperl-l] Celera XML parsers

[Lincoln Stein]

Hi Allen, et al,

For this to work the standard way, the Celera processors should be subclasses 
of an Bio::Variation IO object that will return Bio::VariationI objects when 
the next_variation() method is called.  Looking at what we have now, I see a 
Bio::Variation::IO class, which has a next() method that returns 
Bio::Variation::SeqDiff objects.  Perhaps this does the right thing, but 
perhaps not since it assumes that both variant sequences are available.  
Heikki, could you comment?

Lincoln


On Friday 12 July 2002 06:27 pm, Allen Day wrote:
> Right now, I am working on their SNP format.  My package is currently
> Bio::ClusterIO::celerasnp, creating Bio::Variation::SNP and
> Bio::Variation::Allele objects.
>
> If people are interested in more Celera parsers though, it might be a good
> idea to put them all in one place, under a common namespace.
>
> Once we figure out the namespace, I'll check something in.  Even though it
> doesn't all work yet :).
>
> -Allen
>
> On Fri, 12 Jul 2002, Hilmar Lapp wrote:
> > Cool. Yes yes yes :-)
> >
> > Actually, for which formats?
> >
> > 	-hilmar
> >
> > > -----Original Message-----
> > > From: Allen Day [mailto:allenday@ucla.edu]
> > > Sent: Friday, July 12, 2002 11:29 AM
> > > To: Bioperl
> > > Subject: [Bioperl-l] Celera XML parsers
> > >
> > >
> > > Hi all,
> > >
> > > I'm writing SAX parsers for some Celera pseudo-XML formats.
> > > Is bioperl
> > > the right place to put these?
> > >
> > > -Allen
> > >
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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