Any ideas on how to use this tool in resolving polytomies in IQ-TREE or RAxML outputs? #1
Description
Hi @schultzm, this looks like a very useful tool and thank you for bringing this out. Do you know if this would also work for resolving polytomies in IQ-TREE or RAxML output files? From my quick testing, Budgitree tool (installed via conda on my Ubuntu machine) throws up different errors with both IQ-TREE & RAxML outputs (see below)
budgitree smuggle iqtree.tree > mod_iqtree.tree
Removing polytomies.
Traceback (most recent call last):
File "/home/tools/conda_python3.7_env/bin/budgitree", line 8, in <module>
sys.exit(main())
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/budgitree/__main__.py", line 119, in main
print(next(trees))
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/Bio/Phylo/NewickIO.py", line 308, in to_strings
rawtree = newickize(tree.root) + ";"
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/Bio/Phylo/NewickIO.py", line 301, in newickize
return "(%s)%s" % (",".join(subtrees), label + make_info_string(clade))
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/Bio/Phylo/NewickIO.py", line 300, in <genexpr>
subtrees = (newickize(sub) for sub in clade)
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/Bio/Phylo/NewickIO.py", line 301, in newickize
return "(%s)%s" % (",".join(subtrees), label + make_info_string(clade))
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/Bio/Phylo/NewickIO.py", line 300, in <genexpr>
subtrees = (newickize(sub) for sub in clade)
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/Bio/Phylo/NewickIO.py", line 293, in newickize
unquoted_label = re.match(token_dict["unquoted node label"], label)
File "/home/tools/conda_python3.7_env/lib/python3.7/re.py", line 175, in match
return _compile(pattern, flags).match(string)
RecursionError: maximum recursion depth exceeded
budgitree smuggle RAxML.tree > mod_RAxML.tree
Removing polytomies.
Traceback (most recent call last):
File "/home/tools/conda_python3.7_env/bin/budgitree", line 8, in <module>
sys.exit(main())
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/budgitree/__main__.py", line 87, in main
t = Tree(tree.format("newick"))
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/ete3/coretype/tree.py", line 213, in __init__
quoted_names=quoted_node_names)
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/ete3/parser/newick.py", line 266, in read_newick
return _read_newick_from_string(nw, root_node, matcher, format, quoted_names)
File "/home/tools/conda_python3.7_env/lib/python3.7/site-packages/ete3/parser/newick.py", line 341, in _read_newick_from_string
_read_node_data(closing_internal, current_parent, "internal", matcher, formatcode)
File "/home/tools/conda_python3.7_env/lib/python3.7/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 ':0.15726[100]'