anvi-export-functions

Authors
Requires
Can use
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Export functions of genes from an anvi'o contigs database for a given annotation source.

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)

Requires

contigs-db functions

Can use

genes-of-interest-txt

Provides

functions-txt

Usage

This program takes in a functions artifact to create a functions-txt. Basically, if you want to take the information in your functions artifact out of anvi’o or give it to a fellow anvi’o user (for them to import it into their own project), you get that information using this command.

Simply provide the contigs-db that has been annotated with functions:

anvi-export-functions -c contigs-db

You can also get annotations for only a specific list of sources. For example:

anvi-export-functions -c contigs-db \ --annotation-sources source_1,source_2,source_3

To include positional and contig-level context for each gene in the output, use --include-contig-info. This extends the long-format output with seven additional columns: the contig name, gene start and stop coordinates, strand direction, whether the gene call is partial, contig length, and contig GC content:

anvi-export-functions -c contigs-db \ --include-contig-info \ -o output.txt

Note: --include-contig-info has no effect when used together with --matrix-format.

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-export-functions.

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-export-functions [-h] -c CONTIGS_DB [-o FILE_PATH] [--annotation-sources FUNCTION_ANNOTATION_SOURCE[S]] [-l] [--genes-of-interest FILE] [--matrix-format] [--include-contig-info]

Parameters and their descriptions

options

-c, --contigs-db CONTIGS_DB required: Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-o, --output-file FILE_PATH: File path to store results.
--annotation-sources FUNCTION_ANNOTATION_SOURCE[S]: Get functional annotations for a specific list of annotation sources. You can specify one or more sources by separating them from each other with a comma character (i.e., '--annotation-sources source_1,source_2,source_3'). The default behavior is to return everything
-l, --list-annotation-sources: List available functional annotation sources.
--genes-of-interest FILE: A file with anvi'o gene caller IDs. There should be only one column in the file, and each line should correspond to a unique gene caller id (without a column header).
--matrix-format: Export functions in wide format: one row per gene, sources as columns.
--include-contig-info: Extend the long-format output with positional and contig-level columns: contig name, gene start/stop coordinates, strand direction, partial call flag, contig length, and contig GC content. Has no effect with --matrix-format.

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.