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pwwang / vcfstats

Powerful statistics for VCF files
https://pwwang.github.io/vcfstats/
MIT License
65 stars 15 forks source link

AttributeError: module 'pyparam.params' has no attribute 'vcf' #1

Closed plrlhb12 closed 4 years ago

plrlhb12 commented 4 years ago

This seems a really nice tool in exploring QC of vcf. I wanted to give a try. After I installed it in my mac using pip install vcfstats and run the example vcf file, I got the error as below. Do you have any idea or suggestion on wha the problem and solutions are. Thank you

$ vcfstats --vcf examples/sample.vcf \

--outdir examples/ \ --formula 'COUNT(1) ~ CONTIG' \ --title 'Number of variants on each chromosome' \ --config examples/config.toml

Traceback (most recent call last): File "/Users/pengl7/opt/anaconda3/envs/genomics/bin/vcfstats", line 5, in from vcfstats import main File "/Users/pengl7/opt/anaconda3/envs/genomics/lib/python3.7/site-packages/vcfstats/init.py", line 18, in params.vcf.required = True AttributeError: module 'pyparam.params' has no attribute 'vcf'

pwwang commented 4 years ago

This is due to the pyparam package update. A temporary solution is to install the right version of pyparam:

pip install pyparam==0.3.2

I will work on a version to adapt the latest pyparam

plrlhb12 commented 4 years ago

Thank you for the quick response. Tried again after install the pyparam 0.3.2, but still got the same error message.

pwwang commented 4 years ago

My guess is that pyparam is still not downgraded. Anyways, I will work on it ASAP, and will probably release it today or tmr. I will keep you posted on this post.

pwwang commented 4 years ago

I believe this is fixed at 0.6.0. Please try pip install -U vcfstats to upgrade it.

Closing this, but feel free to reopen if this issue still persists.