vcfstats
vcfstats copied to clipboard
AttributeError: module 'py' has no attribute 'io'
I am getting the following error when running vcfstats and I do not know how I can go about this error. Can someone help with this:
vcfstats --vcf output_filtered.vcf --outdir examples/ --formula 'AAF ~ CONTIG' --title 'Allele frequency on each chromosome (boxplot)' --config examples/config.toml --figtype boxplot
[05/22/23 12:24:43] INFO Combining regions, be reminded that regions should NOT be overlapping ...
[05/22/23 12:24:43] INFO Getting vcf handler by given regions ...
Traceback (most recent call last):
File "/home/okendojo/.local/bin/vcfstats", line 8, in <module>
sys.exit(main())
File "/home/okendojo/.local/lib/python3.8/site-packages/vcfstats/cli.py", line 181, in main
vcf, samples = get_vcf_by_regions(
File "/home/okendojo/.local/lib/python3.8/site-packages/vcfstats/cli.py", line 39, in get_vcf_by_regions
with capture_c_msg("cyvcf2"):
File "/usr/local/Anaconda/envs/py3.8/lib/python3.8/contextlib.py", line 113, in __enter__
return next(self.gen)
File "/home/okendojo/.local/lib/python3.8/site-packages/vcfstats/utils.py", line 65, in capture_c_msg
capture = py.io.StdCaptureFD(out=False, in_=False)
AttributeError: module 'py' has no attribute 'io'
Will this solve the issue:
$ pip install -U py
https://github.com/pytest-dev/pytest/issues/10420#issuecomment-1290697849