user-metabolism

A TXT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

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Provided by

anvi-estimate-metabolism

Required or used by

anvi-compute-metabolic-enrichment

Description

Output text files produced by anvi-estimate-metabolism that describe the presence of user-defined metabolic pathways in a contigs-db.

These files are exactly the same format as those described by kegg-metabolism, but in addition to (or instead of) information on KEGG modules and KEGG Orthologs, they contain information on user-defined metabolic pathways” (and their component enzymes), as described in user-modules-data.

How to get to this output?

You should first read the page on user-modules-data to learn how to define and set up your own metabolic pathways for use in anvi’o. The program that generates this output is anvi-estimate-metabolism, and you should run that program with the --user-modules parameter to make sure the resulting text files contains the information on your user-defined metabolic pathways. There are two main ways to do it (which are also described on the anvi-estimate-metabolism help page):

1. To get files describing user-defined metabolic modules in addition to KEGG modules, just use the --user-modules parameter.

2. To get files describing only user-defined metabolic modules (instead of KEGG stuff), use both --user-modules and --only-user-modules parameters.

What do these files look like?

Check out the kegg-metabolism page for a comprehensive description of the file formats and various options to customize them. The examples on that page show KEGG data, but the format is the same for user-defined data.

Edit this file to update this information.