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