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merenlab / anvio

An analysis and visualization platform for 'omics data
http://merenlab.org/software/anvio
GNU General Public License v3.0
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Metabolic network storage and KEGG database downloading #2123

Closed semiller10 closed 11 months ago

semiller10 commented 11 months ago

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-data and anvi-setup-modelseed-database. Thanks to the efforts of @ivagljiva, anvi-setup-kegg-data now 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.

meren commented 11 months ago

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.