Function: make_kmers

def make_kmers(sequences, kmer_size=3, stride=3, drop_remainder=False) -> list[list[str]]:

Description

Parameters

Parameter	Type	Default	Description
sequences	any iterable containing str	Required	Sequences to encode, can also be dna-parser SequenceReader, pysam FastxFile or Biopython SeqIO.read objects.
kmer_size	int	3	Size of the kmers when splitting the sequences.
stride	int	3	Determines by how many residues the kmer window moves when splitting the sequence.
drop_remainder	bool	False	Determines whether to keep the last kmer with size < kmer_size if the stride and kmer_size do not perfectly split the sequence.

Returns

Type	Description
list[list[str]]	The strings represent the kmers, and the inner list represents the collection of kmer for a sequence.

Examples

import dna_parser as dps

sequences= ["agttcttctc","accttgtg"]
dps.make_kmers(sequences, kmer_size=3, stride=3)

#Output:
# [['agt', 'tct', 'tct', 'c'], ['acc', 'ttg', 'tg']]

sequences= ["agttcttctc","accttgtg"]
dps.make_kmers(sequences, kmer_size=3, stride=3, drop_remainder=True)

#Output:
# [['agt', 'tct', 'tct'], ['acc', 'ttg']]