Metabolic network storage and KEGG database downloading #2123
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…kegg_download_consolidation
…n. we want to encourage people to use the default mode (or read the docs if they really don't want all data so that they can take responsibility for what happens)
…olic-network-storage
…nlab/anvio into metabolic-network-storage
Consolidating our KEGG data download
…ab/anvio into metabolic-network-storage
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This is excellent. Thank you very much for pushing this forward, @semiller10. The only thing I'm realising is that a lot of the docs are missing for the new programs and artifacts this beautiful PR brings in :) I'm about to commit some minor changes to better connect things, but I'm nowhere near addressing the actual need due to my ignorance. |
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This PR enables the storage and output of metabolic reaction networks predicted from KEGG Ortholog annotations of genes. The reaction network is stored in new database tables using the program,
anvi-reaction-network, and can be exported to a JSON-formatted file suitable for inspection and flux balance analysis using the program,anvi-get-metabolic-model-file. Predictions of reactions depend upon KEGG and ModelSEED Biochemistry databases, downloaded using the programs,anvi-setup-kegg-dataandanvi-setup-modelseed-database. Thanks to the efforts of @ivagljiva,anvi-setup-kegg-datanow encompasses all KEGG download and setup operations. Certain KEGG downloads are needed for the new metabolic modeling capabilities, and others are needed for the existing functionality of KO annotation from KOfams and analysis of metabolic module completeness.