

Kmer Vector Functions

• NextGenSeqUtils.corrected_kmer_dist
• NextGenSeqUtils.kmer_count
• NextGenSeqUtils.sparse_aa_kmer_count

# NextGenSeqUtils.kmer_count — Function.

kmer_count(str::String, k::Int)

Count kmers of size k in string, return array with bins from "A...A" to "T...T" and value in each bin corresponding to number of occurences of that kmer within str.

source

# NextGenSeqUtils.sparse_aa_kmer_count — Function.

sparse_aa_kmer_count(str::String, k::Int)

Counts amino acid kmers in string (in all reading frames). k = length of kmer in amino acids. This is sparse and kinda slow.

source

# NextGenSeqUtils.corrected_kmer_dist — Function.

corrected_kmer_dist(kmers1::Array, kmers2::Array; k = nothing)

Compute distance between kmer vectors that is corrected towards edit distance for small differences. The default for k is k = Int(log(4, length(kmers1)))

source

corrected_kmer_dist(k::Int)

Returns function that computes distance between k-mer vectors that is corrected towards edit distance for small differences.

source