[Biopython-dev] Bio.Entrez XML parsing
biopython at maubp.freeserve.co.uk
Wed Apr 2 13:07:59 UTC 2008
On Wed, Apr 2, 2008 at 1:14 PM, João Rodrigues <anaryin at gmail.com> wrote:
> Hey all, I don't know if I'm gonna say something really stupid, because
> really, I haven't read much of the discussion. From what I read you're
> discussing if we can use a parser for the XML given by most entrez methods.
> If you want my advice, I'd use libxml2. I'm currently working with
> efetch/esearch to get PMIDs and Abstracts and I use XML as my return mode
> and libxml2 as my parser. It is quite simple to use and quite faster when
> compared to, for example, minidom. If you need some example code, or some
> hand in this, I'll be more than glad to lend pieces of my code :)
> Best regards!
Do you know how libxml2 compares to the python SAX XML parser for speed?
One big downside is libxml2 would be yet another external dependency
for Biopython. I would be much happier if we could stick to the built
in python libraries.
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