[Biopython] processing XML files in Biopython

[Michiel de Hoon]

--- On Mon, 6/6/11, Peter Cock <p.j.a.cock at googlemail.com> wrote:
> > And, if that is correct, what is the advantage of
> > using Bio.Entrez.parse
> > over using another Python XML lib?
> 
> If you're not scared of XML, not much.
> 
That is a misconception, to say the least.
Bio.Entrez parses the DTD associated with the XML file, and is therefore able to store the information in the XML file as a Python object in a sensible way. In addition, Bio.Entrez.parse can handle multi-gigabyte XML files (such as the ones from the Entrez Gene database). I'd like to see you do that with another Python XML lib.

--Michiel.