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This program calculates the pN/pS ratio for each gene in a contigs-db and outputs it as a pn-ps-data artifact.
The pN/pS ratio (first described in Schloissnig et al. 2012) is the ratio of 2 rates: the rates of non-synonymous (pN) and synonymous (pS) polymorphism. It is analogous to dN/dS, which is the ratio of rates between non-synonymous (dN) and synonymous substitutions between 2 strains/species. We calculate pN/pS from allele frequency obtained through SCVs and SAAVs (see publication in preparation) for exact implementation details.
Firstly, you’ll need to run anvi-gen-variability-profile using the flag
--engine CDN to get a variability-profile-txt for SCVs (single codon variants), which we’ll name
SCVs.txt in this example.
Then you can run this program like so:
anvi-get-pn-ps-ratio -V SCVs.txt \ -c contigs-db \ -o output_dir
A pN/pS value is calculated for each (gene, sample) combo. This will result in a directory called
output_dir that contains several tables that describe each of your genes. See pn-ps-data for more information.
This program has some default filtering choices that you should pay mind to. You can tune these filter options with the following variables:
Edit this file to update this information.
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.