# codonrs
`codonrs` is a small crate for rapidly calculating relative synonymous codon usage (RSCU)
values for coding DNA sequences, for analyses of codon usage bias. The crate can be used
as a command-line utility with the `codonrs` command, or used in other crates via the analysis module.
### Command-line usage
#### Required arguments
**Input**: `-i`/`--input`: A multi-fasta file with the sequences to be analysed as individual
fasta entries. Sequences whose length is not a multiple of three will be ignored
**Output**: `-o`/`--output`: Prefix for the output files. Three files are output by default:
- `prefix`_codon.csv: raw codon counts for each CDS.
- `prefix`_amino_acids.csv: amino acid counts for each CDS, determined from the chosen translation table.
- `prefix`_rscu.csv: calculated RSCU values for each CDS.
#### Optional arguments
**Translation table**: `-t`/`--table`: Integer representing NCBI translation table to be used for codon
counts and RSCU calculation. See tables [here](https://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/index.cgi?chapter=cgencodes).
Defaults to 1: the standard code.
License: GPL-3.0