[Bioperl-l] XML parser preference?

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Wed Aug 9 18:15:06 EDT 2006

Hi Chris,

As I've mentioned in a previous thread, it depends a lot on what your 
module/interface needs to parse from a certain document:


I'm more into tree-based parsing rather than stream-based, but again, it 
depends a lot on personal needs and preferences. If it's possible to 
adapt your modules to use any of the already present parsers, that would 
be great and will avoid adding more pre-requisites to BioPerl.


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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arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM

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