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AlexTISYoung / snipar

Imputation of parental genotypes, inference of sibling IBD segments, family based GWAS, and polygenic score analyses.
MIT License
24 stars 5 forks source link

Warning message of "count_A1" was not set #1

Closed yystat closed 4 years ago

yystat commented 4 years ago

Hello,

Thanks for sharing this package. I'm trying to use it, and when I run either the example codes (https://sibreg.readthedocs.io/en/master/tutorial.html) or run impute_runner.py using my own data, I encountered the following warning. I guess this may not affect the result, but I would like to double check with you.

Thank you very much!

Here is the warning message:

/.local/lib/python3.8/site-packages/pysnptools-0.4.11-py3.8-linux-x86_64.egg/pysnptools/snpreader/bed.py:45: FutureWarning: 'count_A1' was not set. For now it will default to 'False', but in the future it will default to 'True'
  warnings.warn("'count_A1' was not set. For now it will default to 'False', but in the future it will default to 'True'", FutureWarning)

PS: there's a typo in your installation instruction on the main Github page 'python setupy.py install' should be python setup.py install

Josh

AlexTISYoung commented 4 years ago

Hi Josh,

Thanks for your email and feedback. The warning message is not important -- it is a warning from Pysnptools which is used to read .bed files, but it doesn't affect the outcome.

Please let me know if you have any other feedback.

Alex.

On Thu, 16 Jul 2020 at 07:49, Josh notifications@github.com wrote:

Hello,

Thanks for sharing this package. I'm trying to use it, and when I run either the example codes ( https://sibreg.readthedocs.io/en/master/tutorial.html) or run impute_runner.py using my own data, I encountered the following warning. I guess this may not affect the result, but I would like to double check with you.

Thank you very much!

Here is the warning message:

/.local/lib/python3.8/site-packages/pysnptools-0.4.11-py3.8-linux-x86_64.egg/pysnptools/snpreader/bed.py:45: FutureWarning: 'count_A1' was not set. For now it will default to 'False', but in the future it will default to 'True' warnings.warn("'count_A1' was not set. For now it will default to 'False', but in the future it will default to 'True'", FutureWarning)

PS: there's a typo in your installation instruction on the main Github page 'python setupy.py install' should be python setup.py install

Josh

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yystat commented 4 years ago

Ok, thanks!