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

[Jason Stajich]

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
>
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu