[Biopython-dev] Merging Uniprot XML parser?

[Eric Talevich]

On Fri, Nov 5, 2010 at 12:43 PM, Andrea Pierleoni
<andrea at biocomp.unibo.it>wrote:

>
> I've done a couple of testing, from the master biopython branch.
> The uniprot-xml parser successfully parsed the 2010_11 release of uniprot
> containing
> 522,019 entries.
>
> [...]
>
> I have no idea of the performances with jython, and similar derivations of
> python, nor if it works.
>
>
Speaking from my experience with ElementTree in Bio.Phylo -- Jython 2.5's
implementation of xml.etree should work as a drop-in replacement, but it's
painfully slow. However, I've read that the next release of Jython will
include some substantial overall speedups, which should make it more
competitive.

I once tried to get Biopython working on IronPython (on Mono, on Linux), but
didn't succeed. The release I used didn't seem to have a compatible
xml.etree implementation, though the developers may have made progress on
this recently.

-Eric