malva.kmer_processing module

class malva.kmer_processing.FastKmerExtractor

Bases: object

Efficient k-mer extraction and processing class.

malva.kmer_processing.decode_kmer(value, k)

malva.kmer_processing.encode_kmer(kmer)

Encode a DNA k-mer to a numeric value.

malva.kmer_processing.get_kmers_numeric(string, k, remove_noncomplex=False)

Get a list of numerically encoded non-overlapping k-mers from a DNA string.

malva.kmer_processing.get_sliding_kmers_numeric(string, k, remove_noncomplex=False)

Get a list of numerically encoded overlapping k-mers from a DNA string.