[Bioperl-l] XML parser preference?

Chris Fields cjfields at uiuc.edu
Wed Aug 9 19:29:36 EDT 2006


Rob, 

There seems to be a general shift away from using the older XML::Parser and
XML::DOM parsers towards XML::SAX and XML::Twig as the former two are not
under active development.  For SAX parsing, we seem to be moving in the
direction of XML::SAX (the recent transition of SearchIO::blastxml was the
start).  However, nothing has been done for tree-like (DOM) parsing.

In fact, both the XML::DOM and XML::Twig docs recommend XML::LibXML over
XML::DOM.  However, XML::LibXML isn't used AFAIK in Bioperl, and I think
it's more of a burden to use that.

Grr...I wish I had checked bioperl dependencies before I started!  

Chris

> -----Original Message-----
> From: Robert Buels [mailto:rmb32 at cornell.edu]
> Sent: Wednesday, August 09, 2006 5:40 PM
> To: Chris Fields
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] XML parser preference?
> 
> I don't think it really matters. Every parser has its own strengths.
> 
> If you've written something that already works well, but are concerned
> about adding yet another XML parser to bioperl's external dependencies,
> pick a parser that is a.) already being used somewhere else in bioperl
> and b.) requires the fewest changes to your already-working code.
> 
> Since you're already using XML::Simple, which is basically a DOM parser,
> I would say go with another DOM parser that's already being used in
> bioperl. How about XML::DOM?
> 
> Rob
> 
> Chris Fields wrote:
> > All,
> >
> > I am finishing up the EUtilities modules in bioperl-live.  I'm using
> > XML::Simple to grab the IDs and other information from XML returned from
> > NCBI via esearch/elink/epost queries, but I noticed that no other
> Bioperl
> > modules use this particular module.
> >
> > It comes with ActiveState Perl by default (the reason I use it) but I
> found,
> > after the fact, other perl distributions do not include this (Mac OS X
> was
> > one).  I don't necessarily want to lump another XML parser requirement
> for
> > bioperl users on top of the four or so already present, so I'm
> considering
> > changing.
> >
> > I have a preference for SAX (hehe) but XML::Twig might also be an
> option.
> > Any thoughts?
> >
> > Christopher Fields
> > Postdoctoral Researcher - Switzer Lab
> > Dept. of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> >
> 
> --
> Robert Buels
> SGN Bioinformatics Analyst
> 252A Emerson Hall, Cornell University
> Ithaca, NY  14853
> Tel: 503-889-8539
> rmb32 at cornell.edu
> http://www.sgn.cornell.edu




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