mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-04-30 12:00:39 +00:00
Eric Coissac
8c7017a99d
- Update obioptions.Version from "Release 4.4.29" to "/v/ Release v5" - Update version.txt from 4.29 → .30 (automated by Makefile)
21 lines
1.2 KiB
Markdown
21 lines
1.2 KiB
Markdown
## 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:
|
||
```go
|
||
for kmer := range seq.Kmers(3) {
|
||
fmt.Printf("%s\n", string(kmer))
|
||
}
|
||
```
|
||
This yields all 3-mers (e.g., `"ACG"`, `"CGT"`...) in order.
|