[Bioperl-l] XML parser preference?

Robert Buels rmb32 at cornell.edu
Wed Aug 9 18:39:42 EDT 2006

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?


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 
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Robert Buels
SGN Bioinformatics Analyst
252A Emerson Hall, Cornell University
Ithaca, NY  14853
Tel: 503-889-8539
rmb32 at cornell.edu

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