Use ETE module its very easy to use and pretty cool.

I have a CSV with the original names inn one col and new names in the next col. I put this into a dict and rename by traaversing over the tree with ETE.

import csv
from ete3 import Tree, PhyloTree

#read a csv file with species names and abbreviations and replace 
with open('speciesNames.csv', mode='rU') as infile:
    reader = csv.reader(infile)
    mydict = {rows[1]:rows[0] for rows in reader}

for n in leafTree:
    leaf=str(n).replace('\n--','')
    if leaf in mydict.keys():
        newLeafName=mydict[leaf]
        n.name=(newLeafName)
    else:
        print leaf + '\t' + "not in Dict"

leafTree.write(format=9,'abbNamesMetazoanTree.nw')