Poisson-fitter has an option that uses the p-value generated by hypermut to remove sequences and/or positions that present the APOBEC signature.
Currently, hypermut.py prints the contingency table and p-values, and writes the locations of all hypermutated positions to a file. With this implementation, there is no way to pass the p-values to poisson-fitter.py.
I think the best way to address this might be to write the contingency table and p-values to the output file generated by hypermut.py, and have poisson-fitter.py parse this file.
Poisson-fitter has an option that uses the p-value generated by hypermut to remove sequences and/or positions that present the APOBEC signature.
Currently, hypermut.py prints the contingency table and p-values, and writes the locations of all hypermutated positions to a file. With this implementation, there is no way to pass the p-values to poisson-fitter.py.
I think the best way to address this might be to write the contingency table and p-values to the output file generated by hypermut.py, and have poisson-fitter.py parse this file.