Microbial 'omics


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anvi-get-aa-counts [program]

Fetches the number of times each amino acid occurs from a contigs database in a given bin, set of contigs, or set of genes.

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Table of Contents

Provides

aa-frequencies-txt

Requires or uses

splits-txt contigs-db profile-db collection

Usage

Similarly to anvi-get-codon-frequencies, this program counts the number of times each amino acid occurs in a given sequence, whether that’s a collection, bin, set of contigs (listed in a splits-txt), or a set of genes. The output of this is a aa-frequencies-txt.

There are four possible things you can count the amino acid frequencies in:

  • All of the contigs in a contigs-db
  • A series of bins
  • A list of contigs
  • A list of genes

Examples for each are below.

Option 1: all contigs in a contigs-db

To count the amino acids in all of the contigs in a contigs-db, you can just provide the contigs-db of interest, as so:

anvi-get-aa-counts -c contigs-db \ -o path/to/aa-frequencies-txt

Option 2: a series of bins in a collection

To count the amino acid frequencies for a series of bins, you’ll need to provide three additional parameters: the profile-db that you used for binning, the collection that your bins are contained in, and a text file that describes which bins you are interested in. This text file should have only one bin ID per line.

So, your run would look something like this:

anvi-get-aa-counts -c contigs-db \ -o path/to/aa-frequencies-txt \ -p profile-db \ -C collection \ -B my_favorite_bins.txt

my_favorite_bins.txt would look something like this:

bin_00001
bin_00004

Option 3: a list of contigs

Just provide a splits-txt file that lists the contigs you want to look at.

anvi-get-aa-counts -c contigs-db \ -o path/to/aa-frequencies-txt \ --contigs-of-interest splits-txt

Option 4: a list of genes

Just provide a list of gene caller ids, straight into the terminal, like so:

anvi-get-aa-counts -c contigs-db \ -o path/to/aa-frequencies-txt \ --gene-caller-ids gene_1,gene_2,gene_3

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.