[Bioperl-l] FYI - Perl interfaces to XML

Heikki Lehvaslaiho heikki@ebi.ac.uk
Mon, 23 Apr 2001 10:25:13 +0100

Nice timing. I've been thinking about writing to this list about my
recent opinions about XML parsing in Perl. 

I've used XML::Writer for XML output and that still seems to be a good

For writing XML (in Bio::Variation::IO::xml) I've used XML::Node. Some
time ago I wrote to the author about its some annoying shortcomings
and his reply was that he does not have time to work on the package.
In other words, it is now unsupported.

Last week I wrote my first scripts using XML::Twig which seems to me
to be the best general purpose interface to XML parsing. Most
importantly, it gets its name from being able to work on subtrees (=
parsing one database entry at the time) which is crucial to most of
the database parsing type of applications in bioperl. Also, it
contains partial implementation of XPath allowing easy querying of XML

XML::Twig seems to be high on  Kip Hampton's ranking list, too. 

I have not yet finished rewriting Bio::Variation::IO::xml using
XML::Twig but it seems to do the job quite cleanly. 

Since we should have as little dependencies of modules outside of
bioperl, this is an important issue. 

I'd like to drop XML::Node and recommend others too to have a look at


Michael Myers wrote:
> I thought this might be of general interest to the list members...
> Kip Hampton, XML.com's Perl expert in residence, brings us the first
> installment of his definitive guide to XML and Perl. Over the next
> few months, Kip will be surveying the entire XML/Perl landscape.
> This month he covers Perl-specific interfaces to XML, with plenty
> of example code. Educate yourself at
> <http://www.xml.com/pub/a/2001/04/18/perlxmlqstart1.html>.
> -- mpm
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________