[Bioperl-l] XML parsing recommendations in BioPerl?

[Charles Tilford]

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

-- 
Charles Tilford, Bioinformatics-Applied Genomics
Bristol-Myers Squibb PRI, Hopewell 3A039
P.O. Box 5400, Princeton, NJ 08543-5400, (609) 818-3213
charles.tilford@bms.com