usage: frakka.py [-h] [--version] [--kreport KREPORT] [--kout KOUT] [--species SPECIES] [--fof FOF] [--score SCORE] [--counts] [--taxid] [--plot] [--directory DIRECTORY] [--prefix PREFIX]
                 [--delim DELIM]

frakka - a tool to filter Kraken output files and calculate read-level and summary confidence score metrics per classified species

optional arguments:
  -h, --help            show this help message and exit
  --version, -v         show program's version number and exit
  --kreport KREPORT, -k KREPORT
                        Kraken2 report file(s) (comma-separated if multiple, required) (default: None)
  --kout KOUT, -o KOUT  Kraken2 output file(s) (comma-separated if multiple, required, must be in same order as --kreport / -k) (default: None)
  --species SPECIES, -sp SPECIES
                        List of corresponding true / known species names or taxids (comma-separated if multiple, optional, must be in same order as -k and -o files, single species provided assumes
                        all files are same true / known species) (default: None)
  --fof FOF, -f FOF     Tab-separated file of one (-k, -o, -sp)-tuple per line (default: None)
  --score SCORE, -s SCORE
                        Confidence score threshold, only reads / counts higher than this score are reported (default: 0)
  --counts, -c          Report total counts per species with score > --score / -s instead of per-read reporting (default: False)
  --taxid, -t           Species input and output are NCBI taxIDs instead of species names (default: False)
  --plot, -p            NOT IMPLEMENTED Plot distribution of score per species (default: False)
  --directory DIRECTORY, -d DIRECTORY
                        NOT IMPLEMENTED Specify output directory (default: .)
  --prefix PREFIX, -x PREFIX
                        NOT IMPLEMENTED Specify output file prefix (default: .)
  --delim DELIM, -del DELIM
                        Specify output file delimiter (default: )