[Bioperl-l] XML parser preference?

Mauricio Herrera Cuadra arareko at campus.iztacala.unam.mx
Wed Aug 9 20:11:51 EDT 2006


Robert & Chris,

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 (e.g. 
Windows)?

Introducing XML::LibXML as a dependency into the toolkit will probably 
place EUtilities as a module not usable by everyone, especially those 
who use BioPerl in a OS where installing/compiling C dependencies can be 
a headache.

Mauricio.

Chris Fields wrote:
> 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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-- 
MAURICIO HERRERA CUADRA
arareko at campus.iztacala.unam.mx
Laboratorio de Genética
Unidad de Morfofisiología y Función
Facultad de Estudios Superiores Iztacala, UNAM



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