find_leaf_parent.py

from Bio import Phylo

'''
I want to get a dictionary where the keys are every leaf name
and the value is the parental (internal) node of that leaf
'''
tree = Phylo.read(tree_handle, 'newick')
res_dict = {}
for node in tree.find_clades():
    ## if the node is a leaf, the name will be in node.name
    ## if the node is internal, the name will be node.confidence
    print node.name, node.confidence
    ## iterate through the descendet clades (should only be 2)
    for c in node.clades:
        ## if one of them is a leaf aka terminal
        if c.is_terminal():
            ## print leaf name and parent node
            print c, node.confidence
            assert c not in res_dict
            res_dict[c] = node.confidence