Use in Python

You can use the modules provided in the package to call individual methods of you need more customized analysis.

import mtbdiff
#run nucdiff
names = mtbdiff.run_genomes(path, outpath='my_results')
#get the results into a dataframe
struct, snp =  mtbdiff.get_nucdiff_results('my_results', names)
#get region of difference column data
struct['RD'] = struct.apply(mtbdiff.get_region,1)
#get summary
mtbdiff.get_summary(struct)

See the notebooks folder in the repository for examples.