anvi-get-codon-frequencies [program]
Table of Contents
Get amino acid or codon frequencies of genes in a contigs database.
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Authors
Can consume
Can provide
codon-frequencies-txt 
aa-frequencies-txt
Usage
This program calculates the frequency of each codon or amino acid of every gene in your contigs-db.
To run with all standard parameters, simply provide a contigs-db and path for the output file as follows:
anvi-get-codon-frequencies -c contigs-db \ -o name/of/output_file.txt
The output of this is a codon-frequencies-txt that counts the number of times each codon appears in all of your genes.
If instead you want to calculate the data for the amino acids, run
anvi-get-codon-frequencies -c contigs-db \ -o name/of/output_file.txt \ --return-AA-frequencies-instead \ --gene-caller-id MY_FAVORITE_GENE
In this example, the flag gene-caller-id means that it will only count the amino acid frequencies of a single gene, namely MY_FAVORITE_GENE.
You can also return the data as a percent of the total number of codons or amino acids in the gene (with the flag --percent-normalize) or calculate the percent that each codon encoding the same amino acid appears in the gene (for example, 0.4 GCT and 0.6 GCC for alanine) (with the flag --merens-codon-normalization).
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.