anvi-script-gen-user-module-file

Authors
Requires
Provides
Usage
Basics
Automatically generating the module definition
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

This script generates a user-defined module file from a tab-delimited file of enzymes and other input parameters..

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Authors

Iva Veseli

Requires

enzymes-list-for-module

Provides

user-modules-data

Usage

Given an enzymes-list-for-module file, this script will produce a properly-formatted module file for use in anvi-setup-user-modules.

Basics

You should provide this script with an accession ID for your module (which will become the module file name) (-I); a name for the module (-n); a categorization which includes module class, category, and sub-category separated by semicolons (-c); an enzymes-list-for-module file listing the component enzymes, their annotation sources, and their functions (-e); and a definition which puts these enzymes in the proper order (-d):

anvi-script-gen-user-module-file -I “UD0023” \ -n “Frankenstein pathway for demo purposes” \ -c “User modules; Demo set; Frankenstein metabolism” \ -e enzymes-list-for-module \ -d “K01657+K01658 PF06603.14,(COG1362 TIGR01709.2)”

Then this script will produce a properly-formatted module file, which in this case would be called UD0023 and would look like this (see enzymes-list-for-module for the example file containing these enzymes):

ENTRY       UD0023
NAME        Frankenstein pathway for demo purposes
DEFINITION  K01657+K01658 PF06603.14,(COG1362 TIGR01709.2)
ORTHOLOGY   K01657  anthranilate synthase component I [EC:4.1.3.27]
            K01658  anthranilate synthase component II [EC:4.1.3.27]
            PF06603.14  UpxZ
            COG1362  Aspartyl aminopeptidase
            TIGR01709.2  type II secretion system protein GspL
CLASS       User modules; Demo set; Frankenstein metabolism
ANNOTATION_SOURCE  K01657  KOfam
                   K01658  KOfam
                   PF06603.14  METABOLISM_HMM
                   COG1362  COG20_FUNCTION
                   TIGR01709.2  TIGRFAM
\\\

Automatically generating the module definition

The module definition parameter is not required, and if you do not provide one, the definition will be generated with each enzyme in the input file as a different ‘step’ of the module. This option may be especially appropriate for generating what KEGG calls “signature modules”, in which each enzyme is not technically part of a metabolic pathway, but instead the module represents a functionally-related set of enzymes (like all tRNA modification enzymes, for instance).

Here is an example command without the definition parameter:

anvi-script-gen-user-module-file -I “UD0023” \ -n “Frankenstein pathway for demo purposes” \ -c “User modules; Demo set; Frankenstein metabolism” \ -e enzymes-list-for-module \

And here is the module file that this would produce:

ENTRY       UD0023
NAME        Frankenstein pathway for demo purposes
DEFINITION  K01657 K01658 PF06603.14 COG1362 TIGR01709.2
ORTHOLOGY   K01657  anthranilate synthase component I [EC:4.1.3.27]
            K01658  anthranilate synthase component II [EC:4.1.3.27]
            PF06603.14  UpxZ
            COG1362  Aspartyl aminopeptidase
            TIGR01709.2  type II secretion system protein GspL
CLASS       User modules; Demo set; Frankenstein metabolism
ANNOTATION_SOURCE  K01657  KOfam
                   K01658  KOfam
                   PF06603.14  METABOLISM_HMM
                   COG1362  COG20_FUNCTION
                   TIGR01709.2  TIGRFAM
\\\

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-script-gen-user-module-file.

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-script-gen-user-module-file [-h] -e FILE_PATH -I ENTRY_ID -n NAME -c CLASS [-d DEFINITION] [--kegg-data-dir DIR_PATH]

Parameters and their descriptions

REQUIRED INPUT Everything you NEED to make a module definition.

-e, --enzymes-list-for-module FILE_PATH required: A TAB-delimited flat text file that lists the enzymes in your module (one enzyme per line). There are three required columns: an 'enzyme' column that contains the identifier for the enzyme, a 'source' column that contains the annotation source of the enzyme, and an 'orthology' column that contains the functional annotation of the enzyme. Note that the orthology column can be left blank IIF the annotation source is 'KOfam'.
-I, --module-entry ENTRY_ID required: The entry ID for the module. Should be one 'word' (underscores and dashes allowed), and unique to the module.
-n, --module-name NAME required: The name of the module (an arbitrary string - spaces allowed).
-c, --module-class CLASS required: The class of the module. Should be one string with three sections (class, category, subcategory) separated by semi-colons.

OPTIONAL - MODULE DEFINITION If you don't pass a module definition, anvi'o will make each enzyme in the enzymes-list-for-module file a distinct step in the module. Useful if you are not defining a metabolic pathway, but rather a characteristic set of genes (ie, transporters, tRNA modification enzymes, etc).

-d, --module-definition DEFINITION: The definition string of the module in terms of enzyme identifiers, formatted in the KEGG fashion. All enzymes in the definition should be present in the enzymes-list-for-module file. See help pages for instructions on creating the definition.

OPTIONAL - KEGG DATA If you want anvi'o to fill in the ORTHOLOGY of enzymes from source 'KOfam', you might need to tell her where to find any non-default KEGG data.

--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 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.