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Use in Python
Damien Farrell edited this page Oct 15, 2019
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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.