[Biopython-dev] Nexus parser

[Michael Hoffman]

On Tue, 15 Feb 2005, Iddo Friedberg wrote:

> Good News: Frank Kauff & Cymon Cox has contributed a Nexus parser to 
> Biopython, for our next release. It's a mighty useful and nifty package if 
> you are into trees (the phylogenetic ones, not the ones in the forest).

Yay!

> All current Linux distros use a <=2.3 version, and 2.3 does not have
> Sets.

Actually, it does:

$ python2.3
Python 2.3.4 (#1, Feb  2 2005, 12:11:53) 
[GCC 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import sets
>>> sets.Set("biopython")
Set(['b', 'i', 'h', 'o', 'n', 'p', 't', 'y'])

It just doesn't have the built-in sets of Python 2.4:

$ python2.4
Python 2.4 (#1, Nov 30 2004, 11:25:14) 
[GCC 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> set("biopython")
set(['b', 'i', 'h', 'o', 'n', 'p', 't', 'y'])

That said, my vote is to include the module, even in its requiring-2.4
version.
-- 
Michael Hoffman <hoffman at ebi.ac.uk>
European Bioinformatics Institute