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 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.

License: GPL-3.0