Open willmclaren opened 6 years ago
This is due to a deprecation of the scikit-learn module. Downgrading it to a version prior to 0.19 should resolve the issue. We are currently using scikit-learn version 0.18.1 in production.
pip uninstall scikit-learn
pip install scikit-learn==0.18.1
I also noticed that some plots generated using matplotlib version 2 are invalid. You should probably downgrade matplotlib to a version prior to 2 (we use version 1.5.3 in production).
We are planning to update pyGenClean to increase efficiency, enable Python 3 compatibility and use most up-to-date modules. Since this is going to take some time, I recommend just downgrading the two modules as a quick work around.
Thanks @lemieuxl that worked!
One further question, is using plink 1.9 supported (or will it be)? I just tested using it with the above test run and it seems to work OK, and of course much faster (which is the main benefit of 1.9 vs 1.07)
We wanted to wait for an official release of Plink 2 before testing the compatibility with pyGenClean, but I guess it should be for the most part (since the developers say that version 2 is backward compatible with version 1).
I'll leave the ticket open for now, to remind me to fix the scikit-learn issue when updating pyGenClean.
I'm encountering an error while following http://lemieuxl.github.io/pyGenClean/install_linux.html#testing-the-installation
I installed pyGenClean using virtualenv as directed.
Command:
run_pyGenClean --conf test.ini --bfile pyGenClean_test_data/1000G_EUR-MXL_Human610-Quad-v1_ H
Content of test.ini:
Tail of output: