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AndersenLab / VCF-kit

VCF-kit: Assorted utilities for the variant call format
http://www.andersenlab.org
MIT License
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ImportError: cannot import name 'lev' from 'utils' (/Applications/miniconda3/lib/python3.7/site-packages/utils/__init__.py) #23

Closed joswald closed 4 years ago

joswald commented 4 years ago

Any help with this error -- Maybe a python 3 issue?

(base) Jessicas-MacBook-Pro-2:filtering jessicaoswald$ vk setup Traceback (most recent call last): File "/Applications/miniconda3/bin/vk", line 5, in from vcfkit.vk import main File "/Applications/miniconda3/lib/python3.7/site-packages/vcfkit/vk.py", line 24, in from utils import lev, message ImportError: cannot import name 'lev' from 'utils' (/Applications/miniconda3/lib/python3.7/site-packages/utils/init.py)

danielecook commented 4 years ago

@joswald - yes there are issues with python3; What command are you trying to run?

joswald commented 4 years ago

Thanks @danielecook. I was trying to run

vk setup

danielecook commented 4 years ago

@joswald My recommendation is that you set up a custom python2 environment with anaconda/miniconda and use vcf-kit within that environment

conda config --add channels bioconda
conda create -n vcf-kit python=2.7 vcfkit
joswald commented 4 years ago

Perfect. Thanks!