anvi-display-metabolism

Authors
Requires
Can use
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Start the anvi'o interactive interactive for viewing KEGG metabolism data.

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Authors

Iva Veseli

Requires

contigs-db kegg-data kegg-functions

Can use

profile-db collection bin

Provides

interactive

Usage

The purpose of anvi-display-metabolism is to interactively view metabolism estimation data.

This program internally uses anvi-estimate-metabolism to obtain this data for the provided contigs-db.

It is still under development.

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-display-metabolism.

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-display-metabolism [-h] -c CONTIGS_DB [-m] [--kegg-data-dir DIR_PATH] [-p PROFILE_DB] [-C COLLECTION_NAME] [-b BIN_NAME] [-B FILE_PATH] [--module-completion-threshold NUM] [-I IP_ADDR] [-P INT] [--browser-path PATH] [--server-only] [--password-protected]

Parameters and their descriptions

INPUT The minimum you must provide this program is a contigs database. In which case anvi'o will attempt to estimate and display metabolism for all contigs in it, assuming that the contigs database represents a single genome. If the contigs database is actually a metagenome, you should use the `--metagenome` flag to explicitly declare that.

-c, --contigs-db CONTIGS_DB required: Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-m, --metagenome-mode: Treat a given contigs database as an unbinned metagenome rather than treating it as a single genome.
--kegg-data-dir DIR_PATH: The directory path for your KEGG setup, which will include things like KOfam profiles, KEGG MODULE data, and KEGG BRITE data. Anvi'o will try to use the default path if you do not specify anything.

ADDITIONAL INPUT If you also provide a profile database AND a collection name, anvi'o will estimate metabolism separately for each bin in your collection. You can also limit those estimates to a specific bin or set of bins in the collection using the parameters `--bin-id` or `--bin-ids-file`, respectively.

-p, --profile-db PROFILE_DB: Anvi'o profile database
-C, --collection-name COLLECTION_NAME: Collection name.
-b, --bin-id BIN_NAME: Bin name you are interested in.
-B, --bin-ids-file FILE_PATH: Text file for bins (each line should be a unique bin id).

OUTPUT Parameters for controlling estimation output. The output will be TAB-delimited files which by default are prefixed with 'kegg-metabolism', but you can of course change that name here.

--module-completion-threshold NUM: This threshold defines the point at which we consider a KEGG module to be 'complete' or 'present' in a given genome or bin. It is the fraction of steps that must be complete in in order for the entire module to be marked complete. The default is 0.75. Default: 0.75

SERVER CONFIGURATION For power users.

-I, --ip-address IP_ADDR: IP address for the HTTP server. The default ip address (localhost) should work just fine for most. Default: localhost
-P, --port-number INT: Port number to use for anvi'o services. If nothing is declared, anvi'o will try to find a suitable port number, starting from the default port number, 8080.
--browser-path PATH: By default, anvi'o will use your default browser to launch the interactive interface. If you would like to use something else than your system default, you can provide a full path for an alternative browser using this parameter, and hope for the best. For instance we are using this parameter to call Google's experimental browser, Canary, which performs better with demanding visualizations.
--server-only: The default behavior is to start the local server, and fire up a browser that connects to the server. If you have other plans, and want to start the server without calling the browser, this is the flag you need.
--password-protected: If this flag is set, command line tool will ask you to enter a password and interactive interface will be only accessible after entering same password. This option is recommended for shared machines like clusters or shared networks where computers are not isolated.

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.