anvi-setup-modelseed-database

Authors
Requires
Provides
Usage
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

This program downloads and sets up the ModelSEED Biochemistry database..

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Authors

Samuel Miller

Requires

functions

Provides

reaction-ref-data

Usage

This program downloads and sets up the latest version of the ModelSEED Biochemistry database.

The ModelSEED Biochemistry database consists of two tab-delimited files of reaction and compound data, respectively, and is valuable due to harmonization of IDs and properties from multiple reference databases commonly used in metabolic modeling.

anvi-reaction-network relies upon ModelSEED Biochemistry in conjunction with the KEGG Orthology database. KEGG Orthology (KO) protein annotations of genes are associated with predicted enzymatic reactions. These KEGG reactions are cross-referenced to the ModelSEED Biochemistry database to retrieve information on properties including reaction stoichiometry and reversibility. anvi-reaction-network stores reactions and metabolites thereby predicted in the contigs-db for the genome. The program, anvi-setup-kegg-data, sets up the requisite KO database.

Usage

The simplest anvi-setup-modelseed-database command sets up the database in the default anvi’o ModelSEED data directory.

anvi-setup-modelseed-database

A custom directory can be provided instead. Within the provided directory, a subdirectory named ModelSEED is created for storage of the database.

anvi-setup-modelseed-database --dir /path/to/dir

Finally, in conjunction with either of the previous commands, the --reset flag can be used to delete any existing target database directory and its contents before setting up the latest version of the ModelSEED Biochemistry database there.

anvi-setup-modelseed-database --reset

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-setup-modelseed-database.

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

anvi-setup-modelseed-database [-h] [--dir DIR] [--reset]

Parameters and their descriptions

options

--dir DIR: Directory in which a new subdirectory, 'MODELSEED', is created to hold the database files. Without this flag, the database is set up in a default directory within the anvi'o installation (anvio/data/misc/MODELSEED).
--reset: Remove all the previously stored files and start over. If something is feels wrong for some reason and if you believe re-downloading files and setting them up could address the issue, this is the flag that will tell anvi'o to act like a real computer scientist challenged with a computational problem.

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.