[FEATURE] add pathway presence probability to anvi-estimate-metabolism

[dspeth]

The need

thanks for anvi-estimate-metabolism @ivagljiva! I really enjoy how well it works with anvi-compute-enriched-functions. My suggestion (and i know I wasn't the first ;-) ) to make it even better is to add a criterion for presence of a kegg module in a MAG/SAG/genomem in addition to module completion as currently implemented.

The solution

I'd suggest adding the metaPOAP presence/absence probability estimator to the program, so users can choose either a fraction of genes in the module present --module-completion-threshold or a probability that the module is present (or both?) as inclusion criterion. I'd suggest adding this to anvi-compute-enriched-functions as well.

metaPOAP paper: https://academic.oup.com/bioinformatics/article/34/24/4284/5043007, by @lmward and colleagues metaPOAP github repo: https://github.com/lmward/MetaPOAP

Beneficiaries

potentially all users of anvi-estimate-metabolism