Count k-mer frequencies of given `fasta`

optional arguments:
  -h, --help            show this help message and exit
  --fasta filepath      Metagenomic assembly fasta file (default: None)
  --kmers filepath      K-mers frequency tab-delimited table (will skip if
                        file exists) (default: None)
  --size int            k-mer size in bp (default: 5)
  --norm-output filepath
                        Path to normalized kmers table (will skip if file
                        exists) (default: None)
  --norm-method {ilr,clr,am_clr}
                        Normalization method to transform kmer counts prior to
                        PCA and embedding. ilr: isometric log-ratio transform
                        (scikit-bio implementation). clr: center log-ratio
                        transform (scikit-bio implementation). am_clr: center
                        log-ratio transform (Autometa implementation).
                        (default: am_clr)
  --pca-dimensions int  Number of dimensions to reduce to PCA feature space
                        after normalization and prior to embedding (NOTE:
                        Setting to zero will skip PCA step) (default: 50)
  --embedding-output filepath
                        Path to write embedded kmers table (will skip if file
                        exists) (default: None)
  --embedding-method {sksne,bhsne,umap,densmap,trimap}
                        embedding method [sk,bh]sne are corresponding
                        implementations from scikit-learn and tsne,
                        respectively. (default: bhsne)
  --embedding-dimensions int
                        Number of dimensions of which to reduce k-mer
                        frequencies (default: 2)
  --force               Whether to overwrite existing annotations (default:
  --cpus int            num. processors to use. (default: 2)
  --seed int            Seed to set random state for dimension reduction
                        determinism. (default: 42)