[BioPython] Bio.Nexus and Clustal tree files

[Peter (BioPython List)]

Hello again,

I have installed Frank Kauff's recent changes to Bio.Nexus from CVS, and 
have actually got a tree loaded now :)

Here is my example script, which tries to load two tree files created 
using ClustalX 1.83 (files previously sent to Frank off list)

(b) demo.dnd - Clustal guide tree in Newick format, no bootstraps
(b) demo.treb - Clustal NJ tree in Nexus format, with bootstraps

Example code starts here:

from Bio.Nexus import Nexus

for filename in [r"C:\TEMP\nexus\demo.dnd",
              r"C:\TEMP\nexus\demo.treb"] :

     input_file = open(filename,"r")
     n=Nexus.Nexus(input_file)
     input_file.close()

     print "-----------------"
     print "Filename:" + n.filename
     print "Number of taxlabels = %i" % len(n.taxlabels)
     print "Number of trees = %i" % len(n.trees)
     for tree in n.trees :
         print "Tree name: %s"% tree.name
         print "Tree nodes: " +  ", ".join(tree.get_taxa())
print "-----------------"


This gives the following output:

-----------------
Filename:C:\TEMP\nexus\demo.dnd
Number of taxlabels = 0
Number of trees = 0
-----------------
Filename:C:\TEMP\nexus\demo.treb
Number of taxlabels = 0
Number of trees = 1
Tree name: PAUP_1
Tree nodes: V_Harveyi_PATH, B_subtilis_YXEM, B_subtilis_GlnH_homo_YCKK, 
YA80_HAEIN, FLIY_ECOLI, Deinococcus_radiodurans, HISJ_E_COLI, E_coli_GlnH
-----------------

As you can see, loading the ClustalX NEXUS output (*.treb) seems to work 
without trouble (although n.taxlabels is an empty list... is this to be 
expected?).

On the other hand, I don't get the tree for the Clustal guide tree file 
(*.dnd) which is a pain.  Do I need to load these files differently, as 
they are Newick format, not NEXUS format?

Thank you

Peter