CLI Reference

$ CAI --help
Usage: CAI [OPTIONS]

Options:
  -s, --sequence FILE         The sequence to calculate the CAI for.
                              [required]
  -r, --reference FILE        The reference sequences to calculate CAI
                              against.  [required]
  -g, --genetic-code INTEGER  The genetic code to use. Defaults to 11.
  --help                      Show this message and exit.