Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
The following code raises the NewickError. It seems like any notation with all names raises this exception.
from ete3 import Tree
newick = '((D,F)E,(B,H)B);'
t = Tree(newick)
print(t)
Traceback (most recent call last):
File "g:\My Drive\01_Postdoc_HMGU\Python_MyScripts\MIA\Git\Cell_ACDC\cellacdc\test1.py", line 5, in <module>
t = Tree(newick)
File "C:\Users\Frank\.virtualenvs\acdc\lib\site-packages\ete3\coretype\tree.py", line 212, in __init__
read_newick(newick, root_node = self, format=format,
File "C:\Users\Frank\.virtualenvs\acdc\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\Frank\.virtualenvs\acdc\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\Frank\.virtualenvs\acdc\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 'E'
You may want to check other newick loading flags like 'format' or 'quoted_node_names'.
I am using Python 3.9.7 64 bit on Windows 10. Virtual environment created with pyenv. ete3 version 3.1.2 installed with pip.
The following code raises the
NewickError
. It seems like any notation with all names raises this exception.I am using Python 3.9.7 64 bit on Windows 10. Virtual environment created with
pyenv
. ete3 version3.1.2
installed with pip.