[Biopython-dev] Bio.Entrez XML parsing

Peter 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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