anvi-get-aa-counts
Table of Contents
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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Authors
Requires
Can use
splits-txt 
profile-db 
collection 
Provides
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.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-get-aa-counts.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
Parameters and their descriptions
-c, --contigs-dbCONTIGS_DBrequired- Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-o, --output-fileFILE_PATH- File path to store results.
-p, --profile-dbPROFILE_DB- Anvi'o profile database
-C, --collection-nameCOLLECTION_NAME- Collection name.
-B, --bin-ids-fileFILE_PATH- Text file for bins (each line should be a unique bin id).
--contigs-of-interestFILE- A file with contig names. There should be only one column in the file, and each line should correspond to a unique split name.
--gene-caller-idsGENE_CALLER_IDS- Gene caller ids to focus on. Multiple of them can be declared separated by a delimiter (the default is a comma, and if there is no option to change the delimiter, you must use a comma).In anvi-gen-variability-profile, if you declare nothing you will get all genes matching your other filtering criteria. In other programs, you may get everything, nothing, or an error. It really depends on the situation. Fortunately, mistakes are cheap, so it's worth a try.
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.