[Bioperl-l] XML parser preference?
cjfields at uiuc.edu
Thu Aug 10 09:35:21 EDT 2006
Thanks for pointing that out! However, the problem is we want to
keep the number of dependencies down; there are already four XML
parser dependencies for Bioperl (XML::Twig is one, but XML::LibXML
Maybe new modules which require XML parsing stick with four XML
parsers. However, not the current four (XML::DOM, XML::Twig,
Maybe we should pick four XML parsers, each with their own particular
1) XML::SAX (SAX parsing; flexible, can use pure Perl, ExpatXS, etc)
Switch using XML::Parser to XML::SAX (done for
2) XML::LibXML (DOM parsing; maintained, up to date, fast)
Switch using XML::DOM to XML::LibXML
3) XML::Twig (DOM-like, SAX-based) - great for processing 'chunks'
Used in Bio::DB::Taxonomy::entrez
4) XML::Simple (small XML) - very easy to use XML parser
Since they are currently available for most (all?) OS's, shouldn't be
a problem. What do you think Mauricio?
On Aug 10, 2006, at 7:29 AM, Jurgen Pletinckx wrote:
> | I have no doubt that XML::LibXML is a great parser (I've used
> | it a few
> | times), the problem with it is that it runs on top of libxml2's C
> | library. On *nix systems it's fairly simple to have this dependency
> | compiled and running, but what about having it under other OS's
> | Windows)?
> | Introducing XML::LibXML as a dependency into the toolkit will
> | probably
> | place EUtilities as a module not usable by everyone, especially
> | who use BioPerl in a OS where installing/compiling C
> | dependencies can be
> | a headache.
> Regarding XML::LibXML, there does appear to be an up-to-date ppm
> package (which fetches libxml2.dll) at
> (and less than a week since the release of the corresponding
> version to cpan, too.)
> So the threshold for distribution to Windows, at least, is less
> high than it might have been.
> Jurgen Pletinckx
> AlgoNomics NV
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign
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