ModuleNotFoundError: No module named 'CodonUsage'

[tr4ceylee]

Greetings! I am on a MacBook Pro with an M2 chip running Sequoia 15.3. I attempted to install PhageBoost using the github installation steps:

conda create -y -n phageboostENV python=3.11
conda activate phageboostENV
git clone https://github.com/ku-cbd/PhageBoost.git
cd PhageBoost/
python setup.py bdist_wheel
pip install --user .
PhageBoost -h

but got this error:

Traceback (most recent call last):
File "/Users/tpeters/.local/bin/PhageBoost", line 5, in
from PhageBoost.main import main
File "/Users/tpeters/.local/lib/python3.11/site-packages/PhageBoost/init.py", line 1, in
from PhageBoost import get_genecalls, get_predictions, get_matches, calc_features, main, bbcache
File "/Users/tpeters/.local/lib/python3.11/site-packages/PhageBoost/calc_features.py", line 23, in
from CodonUsage import CodonAdaptationIndex, CodonsDict
ModuleNotFoundError: No module named 'CodonUsage'

An issue with biopython in the calc_features.py script?

Please advise!

-Tracey Lee

[cdharrisonmicro]

Hey Tracey! I'm in no way associated with PhageBoost but I had the exact same issue installing PhageBoost on the same system so thought I'd drop the solution I found here :)

Managed to fix it by changing the following on line 23 of the calc_features.py script:

from CodonUsage import CodonAdaptationIndex, CodonsDict # The original code

to

from PhageBoost.CodonUsage import CodonAdaptationIndex, CodonsDict # The updated code that works

And that seemed solved the ModuleNotFoundError :)

Hope it works for you!

Christian

[tr4ceylee]

Hey!

Thank you Christian. Your solution was helpful! It didn't solve the problem all the way for me though - but it worked enough to give me new errors and find the heart of the problem: it was an issue with my XGBoost. Traceback excerpt:

xgboost.core.XGBoostError:
XGBoost Library (libxgboost.dylib) could not be loaded.
Likely causes:

• OpenMP runtime is not installed

  • vcomp140.dll or libgomp-1.dll for Windows
  • libomp.dylib for Mac OSX
  • libgomp.so for Linux and other UNIX-like OSes
    Mac OSX users: Run brew install libomp to install OpenMP runtime.

• You are running 32-bit Python on a 64-bit OS

So I ran:

conda install -c conda-forge py-xgboost

and now PhageBoost -h works as expected. I tried both the original code from line 23 of calc_features.py script and yours, and both work!

I appreciate your help solving this problem.

-Tracey Lee