Export gene calls from an anvi'o contigs database.
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To see the gene callers available in your contigs database, run
anvi-export-gene-calls -c contigs-db \ --list-gene-callers
By default, this list will probably include Prodigal, which identifies genes when creating a contigs-db. For in this example, we’ll use export Prodigal-identified genes. Note that you can also get genes from more than one source by providing several gene-callers in a comma-delimited list.
Then, you can export all of your gene callers in an orderly fashion by running
anvi-export-gene-calls -c contigs-db \ --gene-caller Prodigal \ -o path/to/output
This will put a gene-calls-txt in the path you specified containing all of your Prodigal genes.
If you don’t want to display the amino acid sequences of each gene (they can crowd the file very quickly if you don’t want to see them), just add the flag
Edit this file to update this information.
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.