[SOLVED] Errors loading in a treefile using ETE3

Question

[k.williamson]

Hi there,

I am trying to load a treefile with ete3 using the following:

from ete3 import Tree
t=Tree("ROOT_LGM60.treefile")

However, when I do this, I get the following error messages:

Traceback (most recent call last):
  File "C:/Users/kelse/OneDrive/Documents/Script_Test/leaf_rename.py", line 11, in <module>
    t=Tree('ROOT_LGM60.treefile', format=0)
  File "C:\Users\kelse\Anaconda3\lib\site-packages\ete3\coretype\tree.py", line 213, in __init__
    quoted_names=quoted_node_names)
  File "C:\Users\kelse\Anaconda3\lib\site-packages\ete3\parser\newick.py", line 266, in read_newick
    return _read_newick_from_string(nw, root_node, matcher, format, quoted_names)
  File "C:\Users\kelse\Anaconda3\lib\site-packages\ete3\parser\newick.py", line 341, in _read_newick_from_string
    _read_node_data(closing_internal, current_parent, "internal", matcher, formatcode)
  File "C:\Users\kelse\Anaconda3\lib\site-packages\ete3\parser\newick.py", line 445, in _read_node_data
    raise NewickError("Unexpected newick format '%s' " %subnw[0:50])
ete3.parser.newick.NewickError: Unexpected newick format '100/100:0.1675844217' 
You may want to check other newick loading flags like 'format' or 'quoted_node_names'.

I think it is having an issue with the support values, but I am not sure. This tree was generated using IQ-TREE with aLRT/UFBOOT support. Here is an portion of what the treefile itself looks like:

(0:0.3740934650,(((((((((((1:0.5940078752,46:0.4962741857)100/100:0.1675844217,57:0.6477068763)30.7/67:0.0400940719,88:0.5505298303) ...and so on.

Any help with how to fix this would be appreciated!

Thanks, Kelsey

Answer 1

[cfos4698]

Based on https://groups.google.com/g/etetoolkit/c/8Cl69X7oIg4, you'll have to choose one of the support values to be represented in ete3. You first read in the tree with format=1, which means the tree format is "flexible with internal node names" (http://etetoolkit.org/docs/latest/tutorial/tutorial_trees.html#reading-and-writing-newick-trees), then choose which of the support values from iqtree to use.

tree = Tree("newick", format=1)
for node in tree: 
  if not node.is_leaf():
   node.support = float(node.name.split("/")[1])

You could (e.g.) choose the first value: node.support = float(node.name.split("/")[0])

[k.williamson]

Thank you! This solved the problem