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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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No module named cyvcf2 #5

Closed nuin closed 7 years ago

nuin commented 7 years ago

Hi

After the last update, I am getting an error on imports. Try the machine where I have it installed before and in a new one, fresh and no previous installs. I am on macOS, here is the error

Traceback (most recent call last):
  File "/usr/local/bin/vk", line 7, in <module>
    from vcfkit.vk import main
  File "/usr/local/lib/python2.7/site-packages/vcfkit/vk.py", line 27, in <module>
    from utils.vcf import *
  File "/usr/local/lib/python2.7/site-packages/vcfkit/utils/vcf.py", line 1, in <module>
    from cyvcf2 import VCF as cyvcf2
  File "/usr/local/lib/python2.7/site-packages/cyvcf2/__init__.py", line 1, in <module>
    from .cyvcf2 import (VCF, Variant, Writer, r_ as r_unphased, par_relatedness,
ImportError: No module named cyvcf2
danielecook commented 7 years ago

cyvcf2 is not installing for some reason. I will try to install within a virtual machine and see what happens. Try doing

pip install cyvcf2