[Bioperl-l] Re: XML parsing recommendations in BioPerl?

[Lincoln Stein]

I second Jason's remarks.  The SAX framework is necessary in order for us to 
efficiently pipeline large data sets.

Lincoln

On Saturday 24 August 2002 02:24 pm, Jason Stajich wrote:
> I would stick with XML::Parser::PerlSAX -- it is used in
> Bio::SearchIO::blastxml as well as the GAME parser.  Heikki prefers
> XML::Twig in his hands - so your call on what you think will give you an
> easier time.  I'd prefer you did it in a SAX framework as this will lend
> itself nicely whenever we go to an event based system for sequence
> parsing.  I would rather us go to a event based parsing before too long,
> but it is debateable whether or not that will get done for 1.2.  Someone
> will have to get hot for doing it first I suspect.
>
> -jason
>
> On Wed, 21 Aug 2002, Charles Tilford wrote:
> > Hi Jason,
> >
> > SeqIO::bsml was one of my first XML projects - I agree that it is a
> > bear (awful memory hog). What XML modules will be standard (or
> > pseudo-standard) in BioPerl? It will be a while before I can go back
> > and rehack bsml.pm, but I am now in very early stages of working on an
> > Incyte Foundation parser - initially I was going to use Incyte's API,
> > but using a publically available library will (in addition to avoiding
> > the BioPerl dependancy problem) probably make it more likely that
> > Incyte will allow the thing to be released into the public domain.
> > I'll code that up in whatever is least troublesome, then try to recode
> > bsml.pm.
> >
> > I see that you've used XML::Parser::PerlSAX for the game.pm module -
> > is this the current recommendation?
> >
> > -Charles
> >
> > Jason Stajich wrote:
> > > On Mon, 12 Aug 2002, chris dagdigian wrote:
> > > > The Bundle::BioPerl package does contain Text::Shellwords but it does
> > > > not seem to be working (I noticed this as well this weekend) --
> > > > perhaps there is a problem with something like a newline or tab. I'll
> > > > check this out.
> > > >
> > > > The source of the Bundle::BioPerl.pm file is here:
> > > > http://search.cpan.org/src/CRAFFI/Bundle-BioPerl-2.03/BioPerl.pm
> > > >
> > > > What module has the dependency on XML::DOM ? Does that need to be
> > > > added to the Bundle as well?
> > >
> > > Bio::SeqIO::bsml  --  but I'd very much like to see this re-written not
> > > to use XML::DOM
> > >
> > > > -Chris
> > > >
> > > > Hilmar Lapp wrote:
> > > > > While we're at it, I noticed recently that you need XML::DOM, and
> > > > > at least Makefile.PL doesn't point that out. I don't know about the
> > > > > Bundle though.
> > > > >
> > > > >     -hilmar
> > > > >
> > > > >>-----Original Message-----
> > > > >>From: Brian Osborne [mailto:brian_osborne@cognia.com]
> > > > >>Sent: Monday, August 12, 2002 12:54 PM
> > > > >>To: bioperl-l@bioperl.org
> > > > >>Subject: [Bioperl-l] Does latest Bundle::BioPerl contan
> > > > >>Text::Shellwords?
> > > > >>
> > > > >>
> > > > >>Bioperl-l,
> > > > >>I just used Bundle::BioPerl and it looks like Text::Shellwords
> > > > >> wasn't installed. Is the bundle up-to-date?
> > > > >>Thanks again,
> > > > >>Brian O.
> > >
> > > --
> > > Jason Stajich
> > > Duke University
> > > jason at cgt.mc.duke.edu

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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