[Bioperl-l] BPLite?

[Paul Gordon]

> All that being said, it is definitely good work for you to see how you
> would modify BPlite to parse XML - as a side note - we probably need to
> choose an XML parser that we are going to use consistently across
> bioperl (if one will generally solve all the problems).  Brad Marshall
> chose XML::Parser and XML::Parser::PerlSAX so I see no reason to choose a 
> different one, but XML-philes please correct me if there is reason to
> change. 

That would depend on whether you want to be able to query the XML tree.
PerlSAX is event based, so doesn't handle this; you need a DOM.  A DOM
lets you make sense of more complex XML structures (e.g. MAML).  If large
XML documents are going to be parsed, you'll probably want to use Twig or
something of the sort or else the memory requirements get out of hand.
Unfortunately there doesn't seem to be one right for everything, a
comprimise for most situations would be required.  The only one I have
experience with is Twig, and it handles large documents well.  

My $0.02 CDN.

________________________________________________________________________
Paul Gordon                                     Paul.Gordon@nrc.ca
Genomic Technologies				http://maggie.cbr.nrc.ca
Institute for Marine Biosciences
National Research Council Canada