Parse Labels from newick tree

[sphil]

Hey there,

I am searching for script which extract the node labels from a given newick String. Is there any tool available at the internet, or maybe someone of you guys can help me...


Best,

Phil

[maubp]

There are several options available - which programing language are you happiest with? If Python, then Biopython includes a Newick parser.

Also it would help if you could clarify exactly what you want to get out - just a list of the node labels, throwing away the tree structure?

[sphil]

I just want to have the labels. Tree structure can be thrown away... Python is fine...

[maubp]

If there are internal node labels, do you want the terminal (leaf) names only?

e.g. Using Biopython

from Bio import Phylo
tree = Phylo.read("int_node_labels.nwk", "newick")
for leaf in tree.get_terminals(): print leaf.name

[sphil]

Internal as well would be great...

[maubp]

Internal as well would be great...

For just the internal nodes,

from Bio import Phylo
tree = Phylo.read("int_node_labels.nwk", "newick")
for node in tree.get_nonterminals(): print node.name

For everything try:

from Bio import Phylo
tree = Phylo.read("int_node_labels.nwk", "newick")
for node in tree.find_clades():
    #Don't print anything if there is no name
    if node.name:
        print node.name

[sphil]

thanks alot!