I was previously using KEGG-MAPLE to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued.

Now I'm trying to do something similar but I would like to automate the task.

I want to do the following:

(1) Get KEGG orthologs [KO] for each gene;

(2) Get a table showing that has all the KEGG-modules a KO is associated with

(3) Calculate module completion ratio for groups of genes in my query.

I found a way to identify KOs using kofamscan

What I''m stuck on is how to do (2) from above. This should allow me to calculate (3).**

Is calculating module completion ratio as simple as the following (or is it more complicated):

p = KOs in KEGG module set of interest
q = KOs in query set
r = p ∩ q # This is (p intersect q)
MCR = len(r)/len(p)