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.
installs the latest version of python 3, which doesnt work with ete3, the subsequent conda install ete3... step fails. I had to modify to:
conda create -n ete3 python=3.6
to get the ete3 install step to succeed.
Once ete3 is installed, if i do:
python -c "from ete3 import Tree"
I get the following output:
Traceback (most recent call last):
File "/home/mcphera1/miniconda/envs/pdac_dlp/lib/python3.6/site-packages/ete3/clustering/clustvalidation.py", line 196, in <module>
from scipy import stats
ModuleNotFoundError: No module named 'scipy'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/home/mcphera1/miniconda/envs/pdac_dlp/lib/python3.6/site-packages/ete3/__init__.py", line 61, in <module>
from .clustering.clustertree import *
File "/home/mcphera1/miniconda/envs/pdac_dlp/lib/python3.6/site-packages/ete3/clustering/__init__.py", line 40, in <module>
from .clustertree import *
File "/home/mcphera1/miniconda/envs/pdac_dlp/lib/python3.6/site-packages/ete3/clustering/clustertree.py", line 43, in <module>
from . import clustvalidation
File "/home/mcphera1/miniconda/envs/pdac_dlp/lib/python3.6/site-packages/ete3/clustering/clustvalidation.py", line 199, in <module>
from . import stats
File "/home/mcphera1/miniconda/envs/pdac_dlp/lib/python3.6/site-packages/ete3/clustering/stats.py", line 1933, in <module>
geometricmean = Dispatch ( (lgeometricmean, (ListType, TupleType)), )
NameError: name 'ListType' is not defined
which can be solved by installing scipy:
conda install scipy
However, now if i try to render a tree, ie:
python -c "from ete3 import Tree
t = Tree('((a,b),c);')
t.render('test.png')"
I get the following:
Traceback (most recent call last):
File "<string>", line 3, in <module>
File "/home/mcphera1/miniconda/envs/pdac_dlp/lib/python3.6/site-packages/ete3/coretype/tree.py", line 1354, in render
from ..treeview import drawer
File "/home/mcphera1/miniconda/envs/pdac_dlp/lib/python3.6/site-packages/ete3/treeview/__init__.py", line 42, in <module>
from .main import *
File "/home/mcphera1/miniconda/envs/pdac_dlp/lib/python3.6/site-packages/ete3/treeview/main.py", line 48, in <module>
from PyQt4.QtGui import *
ModuleNotFoundError: No module named 'PyQt4'
pyqt5 is installed, but not pyqt4. Not sure where to get pyqt4.
From the instructions:
installs the latest version of python 3, which doesnt work with ete3, the subsequent
conda install ete3...
step fails. I had to modify to:to get the ete3 install step to succeed.
Once ete3 is installed, if i do:
I get the following output:
which can be solved by installing scipy:
However, now if i try to render a tree, ie:
I get the following:
pyqt5 is installed, but not pyqt4. Not sure where to get pyqt4.