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ksiewert / BetaScan

Genome-wide scan for balancing selection using beta statistic
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the value of Beta1*_std is miss #17

Closed HengLiang1993 closed 1 year ago

HengLiang1993 commented 2 years ago

Hi I run the code: python2 BetaScan.py -i output.beta.txt.gz -onewin -std -theta 0.157 -fold -o betascores-std.txt, and the result show as: Position Beta1 Beta1_std 315639.0 -0.761294 315663.0 0.829734 315677.0 1.213546 315681.0 -0.746679 315685.0 1.253881 315686.0 1.159774 315689.0 0.97459 315690.0 1.25847 315705.0 1.256603 315715.0 1.249427 315725.0 -0.893911 315740.0 0.600665 315953.0 1.309721 316007.0 -0.764854 316008.0 1.27593

The value of Beta1_std is miss.Only show the value of Beta1.

Best

Heng

ksiewert commented 2 years ago

Hello. Sorry for the delayed response. If you wouldn't mind posting a screenshot of your input file around this genomic position, as well as a screenshot of the results file, that would be helpful.

HengLiang1993 commented 1 year ago

Hi My input file is; zcat output.beta.txt.gz | head 315639 152 308 315663 18 330 315677 6 338 315681 162 338 315685 4 338 315686 8 338 315689 14 342 315690 1 344 315705 2 348 315715 1 350

ksiewert commented 1 year ago

Hello. Only Beta1_std should be outputted when the -onewin command is used (see the explanation of the -onewin command here). However, there's a small bug that is causing the header to also contain Beta1, making it look like it should be a 3 column output file. I'm planning to release a new version of BetaScan soon in python3, and will fix this then. Thanks for catching this!

ksiewert commented 1 year ago

This issue should be corrected in the newest release. Let me know if you run into any issues with it.