anvi-reaction-network
Table of Contents
This program generates a metabolic reaction network in an anvi'o contigs or pan database.
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Authors
Requires
Can use
contigs-db 
enzymes-txt 
reaction-ref-data kegg-data
Provides
Usage
This program stores a metabolic reaction-network in a contigs-db or pan-db.
The network consists of data on biochemical reactions predicted to be encoded by the genome or pangenome.
Information on the predicted reactions and the involved metabolites are stored in tables of the contigs-db or pan-db. The program, anvi-get-metabolic-model-file, can be used to export the reaction-network from the database to a reaction-network-json file formatted for input into programs for flux balance analysis.
Setup
anvi-setup-kegg-data downloads, among other files, the binary relations files needed to construct a reaction-network from KEGG Orthology (KO) sequence annotations. The following command sets up the database in a default anvi’o directory.
anvi-setup-kegg-data
anvi-setup-modelseed-database sets up the ModelSEED Biochemistry database, which harmonizes biochemical data from various reference databases, including KEGG. The following command sets up the database in a default anvi’o directory.
anvi-setup-modelseed-database
Download newest available KEGG files
Alternatively, KEGG data can be set up not from a snapshot but by downloading the newest files available from KEGG using the -D flag. In the following command, a higher number of download threads than the default of 1 is provided by -T, which significantly speeds up downloading.
anvi-setup-kegg-data -D -T 5
Install in non-default location
To preserve KEGG data that you already have set up for whatever reason, the new snapshot or download can be placed in a non-default location using the option, --kegg-data-dir.
anvi-setup-kegg-data --kegg-data-dir path/to/other/directory
anvi-reaction-network requires a --kegg-dir argument to seek KEGG data in a non-default location.
Likewise, different versions of the ModelSEED Biochemistry database can be set up in non-default locations and used with the --modelseed-dir argument.
anvi-setup-modelseed-database --dir path/to/other/directory
Usage
From an enzymes file (no contigs database needed)
anvi-reaction-network can build a reaction network directly from a tab-delimited enzymes file — no contigs database required. This is useful when working with custom enzyme lists from transcriptomic/proteomic data, ancestral gene content predictions, or any other source outside of anvi’o’s standard annotation workflow.
The enzymes file must have three columns: gene_id, enzyme_accession, and source. Only rows where source is KOfam are used. This is the same format used by anvi-estimate-metabolism.
anvi-reaction-network --enzymes-txt /path/to/enzymes.txt \ --output-json /path/to/network.json
The resulting JSON file can be directly used by anvi-draw-kegg-pathways via its --reaction-network-json option:
anvi-draw-kegg-pathways --reaction-network-json /path/to/network.json \ -o output_maps/
From a contigs database
anvi-reaction-network takes a either a contigs-db OR a pan-db and genomes-storage-db as required input. Genes stored within the contigs-db or genomes-storage-db must have KO protein annotations, which can be assigned by anvi-run-kegg-kofams.
anvi-reaction-network -c /path/to/contigs-db
If a contigs-db already contains a reaction-network from a previous run of this program, the flag --overwrite-existing-network can overwrite the existing network with a new one. For example, if anvi-run-kegg-kofams is run again on a database using a newer version of KEGG, then anvi-reaction-network should be rerun to update the reaction-network derived from the KO annotations.
anvi-reaction-network -c /path/to/contigs-db \ --overwrite-existing-network
A reaction-network can also be generated from consensus KO annotations of gene clusters. This can be used to understand the conservation or divergence of parts of the metabolic network between organisms in the pangenome.
anvi-reaction-network -p /path/to/pan-db \ -g /path/to/genomes-storage-db
Edit this file to update this information.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-reaction-network.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
Parameters and their descriptions
--enzymes-txtFILE- Path to a tab-delimited enzymes file with required columns 'gene_id', 'enzyme_accession', and 'source'. Rows where 'source' is 'KOfam' are used to build the reaction network. Use '--output-json' to specify where the resulting network file is written.
--output-jsonFILE- Path for the output reaction network JSON file. Required when using '--enzymes-txt'. The file can be loaded by 'anvi-draw-kegg-pathways' via its '--reaction-network-json' option.
-p, --pan-dbPAN_DB- Anvi'o pan database
-g, --genomes-storageGENOMES_STORAGE- Anvi'o genomes storage file
--consensus-thresholdFLOAT- If this argument is provided, then a protein annotation must be assigned to this minimum proportion of genes in a cluster to be imputed to the cluster as a whole. By default, without this argument, the annotation assigned to the most genes becomes the annotation of the cluster (also see --discard-ties). The consensus threshold must be a number from 0 to 1.
--discard-ties- By default, a gene cluster is assigned a protein annotation by finding the protein ortholog that occurs in the greatest number of genes in the cluster (see --consensus-threshold) and arbitrarily choosing one ortholog in case of a tie. With this flag, a tie instead results in an ortholog annotation not being assigned to the cluster.
--kegg-dirPATH- Path to KEGG database directory. If this option is not used, the program expects a database set up in the default location used by 'anvi-setup-kegg-data'.
--modelseed-dirPATH- Path to ModelSEED Biochemistry database directory. If this option is not used, the program expects a database set up in the default location used by 'anvi-setup-modelseed-database'.
Additional Resources
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.