========
kmers.py
========

.. code-block:: bash

	usage: kmers.py

	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:
	                        False)
	  --cpus int            num. processors to use. (default: 2)
	  --seed int            Seed to set random state for dimension reduction
	                        determinism. (default: 42)