How can we get leaf and non-leaf node from NCBITaxa?

[YojanaGadiya]

Dear @jhcepas,

I want to list the terminal and non-terminal nodes for the NCBITaxa tree. Since the tree is an independent object and not part of the PhyloTree class, there is no function to do so. Please can you direct me to an example on where or how this can be done?

Thank You.

[Gullumluvl]

Tree objects have the .get_leaves(), .iter_leaves(), .get_leaf_names(), .iter_leaf_names() methods:

tree = ete3.Tree('(a,b)x,c)r;', format=1)
tree.get_leaf_names()
>>> ['a', 'b', 'c']

tree.get_leaves()
>>> [Tree node 'a' (0x7f54c416a14), Tree node 'b' (0x7f54c416900), Tree node 'c' (0x7f54c416a71)]

To list the internal nodes, iterate all nodes and test if they are (not) a leaf:

for node in tree.traverse():
    if not node.is_leaf():
        print(node)

In case of NCBITaxa module, you may be interested in species nodes, but not subspecies, strains, etc. Use the rank node attribute:

taxatree.get_leaves(is_leaf_fn=lambda node: node.rank == 'species')