Parsing error on Nexus tree generated by iqtree2 (time tree)

[KevinKuchinski]

Hello,

I generated a tree using iqtree2 (time tree). Baltic does not seem to like its Nexus output:

Traceback (most recent call last): File "analysis_with_baltic.py", line 6, in <module> bt.loadNexus(tree_path) File "/Users/kevinkuchinski/mambaforge/envs/tree_grapher/lib/python3.8/site-packages/baltic/baltic.py", line 2134, in loadNexus assert ll,'Failed to find tree string using regular expression' AssertionError: Failed to find tree string using regular expression

I've attached the Nexus file (in txt format).

iqtree2_output.timetree.txt

[RicardoRH96]

Hello, I played around with the tree you uploaded (for the sake of curiosity), and what Baltic doesn't like is the node support annotations added by IQtree2 that look like "Node{number}/{support}".

So two things can be done:

1. Remove the support values (which probably isn't the most useful):
   `import re, baltic as bt
   import matplotlib.pyplot as plt
   import dendropy

with open('iqtree2_output.nex') as fh:
text = fh.read()

clean = re.sub(r'Node(\d+)/\d+', r'Node\1', text)
with open('iqtree2_output.clean.nex', 'w') as fh:
fh.write(clean)

to_resolve = dendropy.TreeList.get(
data=clean,
schema='nexus'
)[0]
to_resolve.resolve_polytomies() #Because the tree is highly polytomic
resolved_nexus = to_resolve.as_string(schema='nexus')
with open('iqtree2_output.clean_resolved.nex', 'w') as fh:
fh.write(resolved_nexus)`

which will produce your regular tree:

2. Change the separator in Node{number}/{support} from a slash to a dot, underscore, or dash:

`import re

with open('iqtree2_output.nex') as fh:
text = fh.read()

rewritten = re.sub(
r'Node(\d+)/(\d+)',
r'Node\1_support\2', # any _, -, or . separator works
text,
)
with open('iqtree2_output.supportsafe.nex', 'w') as fh:
fh.write(rewritten)
`

Then you can load and work with your tree as usual, I added some code to show that it works:

`tree = bt.loadNexus(
'iqtree2_output.supportsafe.nex',
treestring_regex=r'tree\s+\d+(?=\s*=)'
)

ax = plt.subplot(1, 1, 1)

plt.gcf().set_size_inches(10, 10)

support_pattern = re.compile(r'Node(\d+)_support(\d+)')

internal_nodes = []
for obj in tree.Objects:
if obj.is_node() and 'label' in obj.traits:
match = support_pattern.fullmatch(obj.traits['label'])
if match:
obj.traits['node_id'] = int(match.group(1))
obj.traits['support'] = int(match.group(2))
internal_nodes.append(obj)

if internal_nodes:
supports = [n.traits['support'] for n in internal_nodes]
norm = plt.Normalize(vmin=min(supports), vmax=max(supports))
cmap = plt.cm.inferno
sm = plt.cm.ScalarMappable(norm=norm, cmap=cmap)

node_color = lambda n: (
cmap(norm(n.traits['support']))
)

node_size = lambda n: (
20 + (n.traits['support'] / norm.vmax) * 80
)

tree.plotTree(ax=ax, colour='k', linewidth=1)
tree.plotPoints(ax=ax, size=10)
tree.plotPoints(ax=ax, target=lambda node: node.traits.get('support') is not None, colour=node_color, size=node_size)

plt.show()`

This gives you a tree visualization that you can modify to use a different function for color and size.

I hope this helps :)

Maybe @evogytis could add a "type" argument to the loadNexus function so it loads Nexus trees from IQTree2 directly?