etetoolkit
Cannot import name `TreeStyle` from `ete3`
Hi,
not sure what I'm doing wrong, but I am trying to use a minimal example of rendering trees using ete3 version 3.1.2.
from ete3 import Tree
t = Tree( "((a,b),c);" )
t.show()
I get:
ImportError Traceback (most recent call last)
Cell In[36], line 2
1 t = Tree( "((a,b),c);" )
----> 2 t.show()
File ~/opt/anaconda3/envs/analysis/lib/python3.10/site-packages/ete3/coretype/tree.py:1362, in TreeNode.show(self, layout, tree_style, name)
1356 def show(self, layout=None, tree_style=None, name="ETE"):
1357 """
1358 Starts an interactive session to visualize current node
1359 structure using provided layout and TreeStyle.
1360
1361 """
-> 1362 from ..treeview import drawer
1363 drawer.show_tree(self, layout=layout,
1364 tree_style=tree_style, win_name=name)
File ~/opt/anaconda3/envs/analysis/lib/python3.10/site-packages/ete3/treeview/drawer.py:45
41 import signal
43 from .qt import *
---> 45 from .qt4_gui import _GUI, _PropertiesDialog, _BasicNodeActions
47 from . import layouts
48 from .main import save
File ~/opt/anaconda3/envs/analysis/lib/python3.10/site-packages/ete3/treeview/qt4_gui.py:61
...
---> 61 from .. import Tree, TreeStyle
62 import time
64 class _SelectorItem(QGraphicsRectItem):
ImportError: cannot import name 'TreeStyle' from 'ete3' (~/opt/anaconda3/envs/analysis/lib/python3.10/site-packages/ete3/__init__.py)
Other instances of this issue mention the need to install pyqt5 which I did successfully, but did not change the error.
Any ideas would be greatly appreciated!
`from Bio import AlignIO, Phylo
from Bio.Phylo.TreeConstruction import DistanceCalculator, DistanceTreeConstructor
from ete3 import Tree, TreeStyle, TextFace
import matplotlib.pyplot as plt
# Load the alignment from a file in fasta format
alignment_file = "20cd-hit-clust.fa"
alignment = AlignIO.read(alignment_file, "fasta")
# Построение дерева методом Neighbor Joining
calculator = DistanceCalculator('blosum62')
dm = calculator.get_distance(alignment)
nj_constructor = DistanceTreeConstructor(calculator, 'nj')
tree = nj_constructor.build_tree(alignment)
# Сохранение дерева в файл в формате newick
Phylo.write(tree, "my_tree.newick", "newick")
# Создать объект для вывода дерева в формате newick
ete_tree = Tree(tree.to_newick())
# Создать некорневое дерево и настроить его стиль
ts = TreeStyle()
ts.show_leaf_name = False
ts.mode = "c"
ts.arc_start = -180 # установить начальный угол на -180 градусов, чтобы дерево было некорневым
ts.arc_span = 360
ts.scale = 120 # установить масштаб дерева
ts.branch_vertical_margin = 10 # установить отступ между ветвями
ts.title.add_face(TextFace("Unrooted Tree", fsize=20), column=0) # добавить заголовок дерева
# Вывести некорневое дерево в виде изображения
ete_tree.render("my_tree.png", w=1200, h=800, tree_style=ts)
Traceback (most recent call last):
File "C:\Users\rusla\AppData\Roaming\JetBrains\PyCharmCE2021.2\scratches\unrooted_tree.py", line 97, in
Process finished with exit code 1
Hi,
I ran into the same issue (caused by PyQT5) today. It turned out, that it's not enough to install pyqt with pip. To show what error you actually have you should try to print the error where it's caused and silenced:
#/path/to/lib/pythonx.y/site-packages/ete3/__init__.py
try:
from .treeview.svg_colors import *
from .treeview.main import *
from .treeview.faces import *
from .treeview import faces
from .treeview import layouts
except ImportError as e:
pass
#add e.g.
print(e)
in my case the error message was:
libGL.so.1: cannot open shared object file: No such file or directory
meaning, that I was missing the openGL system library. Maybe you should check wheter this is available on your system:
ldconfig -p | grep libGL or locate libGL
Bad news is: I did not find a way to install libGL.so via pip or conda, so if you don't have root access to your machine, users might not be able to solve this on their own.
