Hello everyone,
I downloaded 20/20+ and all packages needed and installed them. I also added the 20/20+ directory to my path variable and I would see the location when I inputted the command $ which 2020plus.py. However, the 20/20+ could not run. The command and error was bellow. I wolud be appreciate it if you could help me solve this problem.
[itmll@node33 pancan_example]$ python2.7 `which 2020plus.py` features -og-test oncogene.txt -tsg-test tsg.txt --summary summary_pancan.txt -o features_pancan.txt
Version: 1.1.2
Command: /data/itmll/yhan/20_20/2020plus-1.1.2/2020plus.py features -og-test oncogene.txt -tsg-test tsg.txt --summary summary_pancan.txt -o features_pancan.txt
**************
AN ERROR HAS OCCURRED: check the log file
**************
Type: < type 'exceptions.ImportError'>
Exception: cannot import name random_choice_csc
Traceback:
File "/data/itmll/yhan/20_20/2020plus-1.1.2/2020plus.py", line 329, in <module>
import src.classify.python.classifier
File "/data/itmll/yhan/20_20/2020plus-1.1.2/src/classify/python/classifier.py", line 2, in <module>
from src.classify.python.dummy_clf import DummyClf
File "/data/itmll/yhan/20_20/2020plus-1.1.2/src/classify/python/dummy_clf.py", line 1, in <module>
from sklearn.dummy import DummyClassifier
File "/public/software/bin/python2.72/lib/python2.7/site-packages/sklearn/dummy.py", line 16, in <module>
from .utils.random import random_choice_csc
I was wandering how to run 20/20+ correctly.
1 answer
Python packages dependencies can be tricky, and installing the packages with different orders can have different results. I suggest you use use the dependencies file provided with 20/20+, and install as instructed in the manual:
pip install -r requirements.txt
In addition, I would use virtualenv, so it is easy to start over if the install is messed up.
Log in to answer this question.
what is 20/20+ ?
Probably this package: https://github.com/KarchinLab/2020plus.