equivalent-compounds-txt

A TXT-type anvi’o artifact. This artifact can be generated, used, and/or exported by anvi’o. It can also be provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.

Required or used by

anvi-predict-metabolic-exchanges

Description

This file describes pairs of ModelSEED compound IDs that should be considered equivalent to each other for the purposes of predicting potential metabolic exchanges with anvi-predict-metabolic-exchanges.

Example file

The file should be tab-delimited and have four columns. The first two columns contain the pair of ModelSEED compound IDs that you consider equivalent, and the second two columns contain their respective human-readable names (for convenience when reading the file).

compound_id	equivalent_id	name	equivalent_name
cpd00035	cpd01003	L-Alanine	Alanine
cpd00039	cpd19182	L-Lysine	Lysine
cpd00041	cpd19181	L-Aspartate	Aspartate

Pro Tip: generating the file automatically

If you run anvi-predict-metabolic-exchanges with the --use-equivalent-amino-acids flag, it will create a file of this type containing the set of amino acid compound equivalents it automatically finds in the ModelSEED database:

You can modify the resulting output file as you want to remove or add new compound equivalents and make a custom set that can be passed to anvi-predict-metabolic-exchanges with the --custom-equivalent-compounds-file parameter.

Edit this file to update this information.