Expand description
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 mod.
§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.
Defaults to 1: the standard code.