Stepwise completeness, module copy number, and a bunch of other useful updates to metabolism #1927
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…y in the dictionary
…e this data in the hits_in_modules output mode
…rate for paths with duplicate kos. the problem was that we put the hit counts into a dictionary and used the number of keys as path length, thereby ignoring duplicate kos
…to be split into only their essential components. otherwise we couldn't look up their hit counts in the module dictionary
… as completeness except for modules defined by other modules
…modules that don't have complete paths
… realized it while writing up the documentation)
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This PR will be my last major update to the metabolism code for the next few months. It includes the following updates:
--add-copy-numberis used to add this data to long format output, or to generate additional matrix files with these metricsanvi-compute-metabolic-enrichmentuses pathwise completeness by default, but you can request to use stepwise completeness instead with the new flag--use-stepwise-completenessanvi-setup-kegg-kofamshas been refactored to better separate download of data from database setup. There are two new flags,--only-downloadand--only-database, for better control of what is done when the-Dflag is used. This is mostly useful for quick testing: now you can download the data once using--only-downloadand run the database setup multiple times using--only-databaseanvi-setup-kegg-kofams. It includes BRITE data and modules db v4The metabolism suite of
anvi-self-test+ documentation have been updated to reflect these new changes. The PR passes the self test. Feel free to check the help pages for descriptions of these new features :)