Microbial 'omics


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anvi-export-gene-calls [program]

Export gene calls from an anvi'o contigs database.

See program help menu or go back to the main page of anvi’o programs and artifacts.

Table of Contents

Provides

gene-calls-txt

Requires or uses

contigs-db

Usage

This program exports your gene calls given a contigs-db and a gene caller. The output of this is a gene-calls-txt.

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 --skip-sequence-reporting

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.