anvi-export-gene-calls

Export gene calls from an anvi'o contigs database.

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Authors

Can consume

contigs-db

Can provide

gene-calls-txt

Usage

The purpose of this program is to exports your gene calls in a given contigs-db and a gene caller, in the form of a gene-calls-txt.

To see the gene callers available in your contigs database, you can use anvi-db-info or use this program with the following flag:

Running this will export all of your gene calls identified by the gene caller prodigal (assuming it is in your contigs-db:

You can export genes from more gene callers by providing a comma-separated list of gene caller names.

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), you can add the following flag:

Advanced uses

This program can take a lot of time and memory when working with very large contigs-db files (such as those that are more than 10 Gb in file size or more than 10 million contigs).

In that case you can export your gene calls the following way within minutes and a small memory space.

First open your contigs-db:

Then run these lines,

You can also continue with these lines to get the amino acid sequences for them:

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.