obitools4/autodoc/docmd/pkg/obiseq/kmers.md

BioSequence.Kmers(k int) — Semantic Description

The Kmers method is a generator function that yields all contiguous k-length subsequences (called k-mers) from a biological sequence (BioSequence).

• It operates on []byte data, assuming the underlying sequence is stored as a byte slice (e.g., DNA bases A, C, G, T).
• Uses Go’s new iterator protocol (iter.Seq[[]byte]) for memory-efficient, lazy evaluation.
• Validates input: returns an empty iterator if k ≤ 0 or exceeds sequence length.
• Iterates linearly from index i = 0 to len(seq) - k, extracting slices of length k.
• Each yielded value is a non-copying slice view (efficient, but mutable if original data changes).
• Supports early termination: the consumer can stop iteration by returning false from the yield callback.
• Designed for downstream tasks like sequence analysis, motif discovery, or hashing (e.g., in k-mer counting).
• Does not handle reverse-complement or ambiguous bases—assumes raw sequence input.

Usage example:

for kmer := range seq.Kmers(3) {
    fmt.Printf("%s\n", string(kmer))
}

This yields all 3-mers (e.g., "ACG", "CGT"...) in order.