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AlexandrovLab / SigProfilerMatrixGenerator

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.
BSD 2-Clause "Simplified" License
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SigProfilerMatrixGenerator 1.2.26 is still broken: binomtest does not take a parameter "x" #181

Closed toddajohnson closed 2 months ago

toddajohnson commented 4 months ago

I just installed and ran SigProfilerMatrixGenerator 1.2.26, and it fails with an error that binomtest does not take a parameter x. The points in MutationMatrixGenerator.py all use binomtest(x=. According to https://docs.scipy.org/doc/scipy/reference/generated/scipy.stats.binomtest.html, binomtest takes a parameter k for the number of successes.

mdbarnesUCSD commented 3 months ago

Hi @toddajohnson,

Thanks for filling out and issue. Apologies for the oversight with the v1.2.26 update. We will include a patch for this in the next update.

Changes being made are on branch i181.

Thanks again!