mirror of
https://github.com/metabarcoding/obitools4.git
synced 2026-03-25 13:30:52 +00:00
Refactor SuperKmer extraction to use iterator pattern
This commit refactors the SuperKmer extraction functionality to use Go's new iterator pattern. The ExtractSuperKmers function is now implemented as a wrapper around a new IterSuperKmers iterator function, which yields results one at a time instead of building a complete slice. This change provides better memory efficiency and more flexible consumption of super k-mers. The functionality remains the same, but the interface is now more idiomatic and efficient for large datasets.
This commit is contained in:
Eric Coissac
@@ -447,141 +447,6 @@ func IterCanonicalKmers(seq []byte, k int) iter.Seq[uint64] {
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}
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}
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}
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// SuperKmer represents a maximal subsequence where all consecutive k-mers
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// share the same minimizer. A minimizer is the smallest canonical m-mer
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// among the (k-m+1) m-mers contained in a k-mer.
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type SuperKmer struct {
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Minimizer uint64 // The canonical minimizer value (normalized m-mer)
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Start int // Starting position in the original sequence (0-indexed)
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End int // Ending position (exclusive, like Go slice notation)
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Sequence []byte // The actual DNA subsequence [Start:End]
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}
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// dequeItem represents an element in the monotone deque used for
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// tracking minimizers in a sliding window.
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type dequeItem struct {
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position int // Position of the m-mer in the sequence
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canonical uint64 // Canonical (normalized) m-mer value
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}
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// ExtractSuperKmers extracts super k-mers from a DNA sequence.
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// A super k-mer is a maximal subsequence where all consecutive k-mers
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// share the same minimizer. The minimizer of a k-mer is the smallest
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// canonical m-mer among its (k-m+1) constituent m-mers.
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//
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// The algorithm uses:
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// - Simultaneous forward/reverse m-mer encoding for O(1) canonical m-mer computation
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// - Monotone deque for O(1) amortized minimizer tracking per position
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//
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// The maximum k-mer size is 31 (using 62 bits), leaving the top 2 bits
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// available for error markers if needed.
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//
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// Parameters:
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// - seq: DNA sequence as a byte slice (case insensitive, supports A, C, G, T, U)
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// - k: k-mer size (must be between m+1 and 31)
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// - m: minimizer size (must be between 1 and k-1)
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// - buffer: optional pre-allocated buffer for results. If nil, a new slice is created.
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//
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// Returns:
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// - slice of SuperKmer structs representing maximal subsequences
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// - nil if parameters are invalid or sequence is too short
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//
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// Time complexity: O(n) where n is the sequence length
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// Space complexity: O(k-m+1) for the deque + O(number of super k-mers) for results
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func ExtractSuperKmers(seq []byte, k int, m int, buffer *[]SuperKmer) []SuperKmer {
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if m < 1 || m >= k || k < 2 || k > 31 || len(seq) < k {
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return nil
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}
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var result []SuperKmer
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if buffer == nil {
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estimatedSize := len(seq) / k
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if estimatedSize < 1 {
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estimatedSize = 1
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}
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result = make([]SuperKmer, 0, estimatedSize)
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} else {
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result = (*buffer)[:0]
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}
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deque := make([]dequeItem, 0, k-m+1)
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mMask := uint64(1)<<(m*2) - 1
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rcShift := uint((m - 1) * 2)
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var fwdMmer, rvcMmer uint64
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for i := 0; i < m-1 && i < len(seq); i++ {
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code := uint64(__single_base_code__[seq[i]&31])
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fwdMmer = (fwdMmer << 2) | code
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rvcMmer = (rvcMmer >> 2) | ((code ^ 3) << rcShift)
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}
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superKmerStart := 0
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var currentMinimizer uint64
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firstKmer := true
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for pos := m - 1; pos < len(seq); pos++ {
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code := uint64(__single_base_code__[seq[pos]&31])
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fwdMmer = ((fwdMmer << 2) | code) & mMask
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rvcMmer = (rvcMmer >> 2) | ((code ^ 3) << rcShift)
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canonical := fwdMmer
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if rvcMmer < fwdMmer {
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canonical = rvcMmer
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}
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mmerPos := pos - m + 1
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if pos >= k-1 {
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windowStart := pos - k + 1
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for len(deque) > 0 && deque[0].position < windowStart {
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deque = deque[1:]
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}
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}
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for len(deque) > 0 && deque[len(deque)-1].canonical >= canonical {
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deque = deque[:len(deque)-1]
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}
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deque = append(deque, dequeItem{position: mmerPos, canonical: canonical})
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if pos >= k-1 {
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newMinimizer := deque[0].canonical
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kmerStart := pos - k + 1
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if firstKmer {
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currentMinimizer = newMinimizer
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firstKmer = false
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} else if newMinimizer != currentMinimizer {
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endPos := kmerStart + k - 1
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superKmer := SuperKmer{
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Minimizer: currentMinimizer,
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Start: superKmerStart,
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End: endPos,
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Sequence: seq[superKmerStart:endPos],
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}
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result = append(result, superKmer)
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superKmerStart = kmerStart
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currentMinimizer = newMinimizer
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}
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}
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}
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if !firstKmer {
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superKmer := SuperKmer{
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Minimizer: currentMinimizer,
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Start: superKmerStart,
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End: len(seq),
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Sequence: seq[superKmerStart:],
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}
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result = append(result, superKmer)
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}
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return result
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}
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// ReverseComplement computes the reverse complement of an encoded k-mer.
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// The k-mer is encoded with 2 bits per nucleotide (A=00, C=01, G=10, T=11).
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// The complement is: A↔T (00↔11), C↔G (01↔10), which is simply XOR with 11.
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59
pkg/obikmer/superkmer.go
Normal file
59
pkg/obikmer/superkmer.go
Normal file
@@ -0,0 +1,59 @@
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package obikmer
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// SuperKmer represents a maximal subsequence where all consecutive k-mers
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// share the same minimizer.
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type SuperKmer struct {
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Minimizer uint64 // The canonical minimizer value (normalized m-mer)
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Start int // Starting position in the original sequence (0-indexed)
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End int // Ending position (exclusive, like Go slice notation)
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Sequence []byte // The actual DNA subsequence [Start:End]
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}
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// dequeItem represents an element in the monotone deque used for
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// tracking minimizers in a sliding window.
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type dequeItem struct {
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position int // Position of the m-mer in the sequence
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canonical uint64 // Canonical (normalized) m-mer value
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}
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// ExtractSuperKmers extracts super k-mers from a DNA sequence.
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// A super k-mer is a maximal subsequence where all consecutive k-mers
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// share the same minimizer. The minimizer of a k-mer is the smallest
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// canonical m-mer among its (k-m+1) constituent m-mers.
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//
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// This function uses IterSuperKmers internally and collects results into a slice.
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//
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// Parameters:
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// - seq: DNA sequence as a byte slice (case insensitive, supports A, C, G, T, U)
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// - k: k-mer size (must be between m+1 and 31)
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// - m: minimizer size (must be between 1 and k-1)
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// - buffer: optional pre-allocated buffer for results. If nil, a new slice is created.
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//
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// Returns:
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// - slice of SuperKmer structs representing maximal subsequences
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// - nil if parameters are invalid or sequence is too short
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//
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// Time complexity: O(n) where n is the sequence length
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// Space complexity: O(k-m+1) for the deque + O(number of super k-mers) for results
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func ExtractSuperKmers(seq []byte, k int, m int, buffer *[]SuperKmer) []SuperKmer {
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if m < 1 || m >= k || k < 2 || k > 31 || len(seq) < k {
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return nil
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}
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var result []SuperKmer
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if buffer == nil {
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estimatedSize := len(seq) / k
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if estimatedSize < 1 {
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estimatedSize = 1
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}
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result = make([]SuperKmer, 0, estimatedSize)
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} else {
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result = (*buffer)[:0]
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}
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for sk := range IterSuperKmers(seq, k, m) {
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result = append(result, sk)
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}
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return result
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}
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215
pkg/obikmer/superkmer_iter.go
Normal file
215
pkg/obikmer/superkmer_iter.go
Normal file
@@ -0,0 +1,215 @@
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package obikmer
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import (
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"fmt"
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"iter"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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)
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// IterSuperKmers returns an iterator over super k-mers extracted from a DNA sequence.
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// It uses the same algorithm as ExtractSuperKmers but yields super k-mers one at a time.
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//
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// Parameters:
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// - seq: DNA sequence as a byte slice (case insensitive, supports A, C, G, T, U)
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// - k: k-mer size (must be between m+1 and 31)
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// - m: minimizer size (must be between 1 and k-1)
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//
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// Returns:
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// - An iterator that yields SuperKmer structs
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//
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// Example:
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//
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// for sk := range IterSuperKmers(sequence, 21, 11) {
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// fmt.Printf("SuperKmer at %d-%d with minimizer %d\n", sk.Start, sk.End, sk.Minimizer)
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// }
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func IterSuperKmers(seq []byte, k int, m int) iter.Seq[SuperKmer] {
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return func(yield func(SuperKmer) bool) {
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if m < 1 || m >= k || k < 2 || k > 31 || len(seq) < k {
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return
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}
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deque := make([]dequeItem, 0, k-m+1)
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mMask := uint64(1)<<(m*2) - 1
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rcShift := uint((m - 1) * 2)
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var fwdMmer, rvcMmer uint64
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for i := 0; i < m-1 && i < len(seq); i++ {
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code := uint64(__single_base_code__[seq[i]&31])
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fwdMmer = (fwdMmer << 2) | code
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rvcMmer = (rvcMmer >> 2) | ((code ^ 3) << rcShift)
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}
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superKmerStart := 0
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var currentMinimizer uint64
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firstKmer := true
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for pos := m - 1; pos < len(seq); pos++ {
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code := uint64(__single_base_code__[seq[pos]&31])
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fwdMmer = ((fwdMmer << 2) | code) & mMask
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rvcMmer = (rvcMmer >> 2) | ((code ^ 3) << rcShift)
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canonical := fwdMmer
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if rvcMmer < fwdMmer {
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canonical = rvcMmer
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}
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mmerPos := pos - m + 1
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if pos >= k-1 {
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windowStart := pos - k + 1
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for len(deque) > 0 && deque[0].position < windowStart {
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deque = deque[1:]
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}
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}
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for len(deque) > 0 && deque[len(deque)-1].canonical >= canonical {
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deque = deque[:len(deque)-1]
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}
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deque = append(deque, dequeItem{position: mmerPos, canonical: canonical})
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if pos >= k-1 {
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newMinimizer := deque[0].canonical
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kmerStart := pos - k + 1
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if firstKmer {
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currentMinimizer = newMinimizer
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firstKmer = false
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} else if newMinimizer != currentMinimizer {
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endPos := kmerStart + k - 1
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superKmer := SuperKmer{
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Minimizer: currentMinimizer,
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Start: superKmerStart,
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End: endPos,
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Sequence: seq[superKmerStart:endPos],
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}
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if !yield(superKmer) {
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return
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}
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superKmerStart = kmerStart
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currentMinimizer = newMinimizer
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}
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}
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}
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if !firstKmer {
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superKmer := SuperKmer{
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Minimizer: currentMinimizer,
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Start: superKmerStart,
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End: len(seq),
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Sequence: seq[superKmerStart:],
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}
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yield(superKmer)
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}
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}
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}
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// ToBioSequence converts a SuperKmer to a BioSequence with metadata.
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//
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// The resulting BioSequence contains:
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// - ID: "{parentID}_superkmer_{start}_{end}"
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// - Sequence: the actual DNA subsequence
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// - Attributes:
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// - "minimizer_value" (uint64): the canonical minimizer value
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// - "minimizer_seq" (string): the DNA sequence of the minimizer
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// - "k" (int): the k-mer size
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// - "m" (int): the minimizer size
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// - "start" (int): starting position in original sequence
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// - "end" (int): ending position in original sequence
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// - "parent_id" (string): ID of the parent sequence
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//
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// Parameters:
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// - k: k-mer size used for extraction
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// - m: minimizer size used for extraction
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// - parentID: ID of the parent sequence
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// - parentSource: source field from the parent sequence
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//
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// Returns:
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// - *obiseq.BioSequence: A new BioSequence representing this super k-mer
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func (sk *SuperKmer) ToBioSequence(k int, m int, parentID string, parentSource string) *obiseq.BioSequence {
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// Create ID for the super-kmer
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var id string
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if parentID != "" {
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id = fmt.Sprintf("%s_superkmer_%d_%d", parentID, sk.Start, sk.End)
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} else {
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id = fmt.Sprintf("superkmer_%d_%d", sk.Start, sk.End)
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}
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// Create the BioSequence
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seq := obiseq.NewBioSequence(id, sk.Sequence, "")
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// Copy source from parent
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if parentSource != "" {
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seq.SetSource(parentSource)
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}
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// Set attributes
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seq.SetAttribute("minimizer_value", sk.Minimizer)
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// Decode the minimizer to get its DNA sequence
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minimizerSeq := DecodeKmer(sk.Minimizer, m, nil)
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seq.SetAttribute("minimizer_seq", string(minimizerSeq))
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seq.SetAttribute("k", k)
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seq.SetAttribute("m", m)
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seq.SetAttribute("start", sk.Start)
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seq.SetAttribute("end", sk.End)
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if parentID != "" {
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seq.SetAttribute("parent_id", parentID)
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}
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return seq
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}
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// SuperKmerWorker creates a SeqWorker that extracts super k-mers from a BioSequence
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// and returns them as a slice of BioSequence objects.
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//
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// The worker copies the source field from the parent sequence to all extracted super k-mers.
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//
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// Parameters:
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// - k: k-mer size (must be between m+1 and 31)
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// - m: minimizer size (must be between 1 and k-1)
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//
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// Returns:
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// - SeqWorker: A worker function that can be used in obiiter pipelines
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//
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// Example:
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//
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// worker := SuperKmerWorker(21, 11)
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// iterator := iterator.MakeIWorker(worker, false)
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func SuperKmerWorker(k int, m int) obiseq.SeqWorker {
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return func(seq *obiseq.BioSequence) (obiseq.BioSequenceSlice, error) {
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if seq == nil {
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return obiseq.BioSequenceSlice{}, nil
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}
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// Validate parameters
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if m < 1 || m >= k || k < 2 || k > 31 {
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return obiseq.BioSequenceSlice{}, fmt.Errorf(
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"invalid parameters: k=%d, m=%d (need 1 <= m < k <= 31)",
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k, m)
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}
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sequence := seq.Sequence()
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if len(sequence) < k {
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return obiseq.BioSequenceSlice{}, nil
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}
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parentID := seq.Id()
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parentSource := seq.Source()
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// Extract super k-mers and convert to BioSequences
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result := make(obiseq.BioSequenceSlice, 0)
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for sk := range IterSuperKmers(sequence, k, m) {
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bioSeq := sk.ToBioSequence(k, m, parentID, parentSource)
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result = append(result, bioSeq)
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}
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return result, nil
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}
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}
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82
pkg/obikmer/superkmer_iter_test.go
Normal file
82
pkg/obikmer/superkmer_iter_test.go
Normal file
@@ -0,0 +1,82 @@
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package obikmer
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import (
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"testing"
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)
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func TestIterSuperKmers(t *testing.T) {
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seq := []byte("ACGTACGTGGGGAAAA")
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k := 5
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m := 3
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count := 0
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for sk := range IterSuperKmers(seq, k, m) {
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count++
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t.Logf("SuperKmer %d: Minimizer=%d, Start=%d, End=%d, Seq=%s",
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count, sk.Minimizer, sk.Start, sk.End, string(sk.Sequence))
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// Verify sequence boundaries
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if sk.Start < 0 || sk.End > len(seq) {
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t.Errorf("Invalid boundaries: Start=%d, End=%d, seqLen=%d",
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sk.Start, sk.End, len(seq))
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}
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// Verify sequence content
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if string(sk.Sequence) != string(seq[sk.Start:sk.End]) {
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t.Errorf("Sequence mismatch: expected %s, got %s",
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string(seq[sk.Start:sk.End]), string(sk.Sequence))
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}
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}
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if count == 0 {
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t.Error("No super k-mers extracted")
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}
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t.Logf("Total super k-mers extracted: %d", count)
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}
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func TestIterSuperKmersVsSlice(t *testing.T) {
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seq := []byte("ACGTACGTGGGGAAAAACGTACGT")
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k := 7
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m := 4
|
||||
|
||||
// Extract using slice version
|
||||
sliceResult := ExtractSuperKmers(seq, k, m, nil)
|
||||
|
||||
// Extract using iterator version
|
||||
var iterResult []SuperKmer
|
||||
for sk := range IterSuperKmers(seq, k, m) {
|
||||
iterResult = append(iterResult, sk)
|
||||
}
|
||||
|
||||
// Compare counts
|
||||
if len(sliceResult) != len(iterResult) {
|
||||
t.Errorf("Different number of super k-mers: slice=%d, iter=%d",
|
||||
len(sliceResult), len(iterResult))
|
||||
}
|
||||
|
||||
// Compare each super k-mer
|
||||
for i := 0; i < len(sliceResult) && i < len(iterResult); i++ {
|
||||
slice := sliceResult[i]
|
||||
iter := iterResult[i]
|
||||
|
||||
if slice.Minimizer != iter.Minimizer {
|
||||
t.Errorf("SuperKmer %d: different minimizers: slice=%d, iter=%d",
|
||||
i, slice.Minimizer, iter.Minimizer)
|
||||
}
|
||||
|
||||
if slice.Start != iter.Start || slice.End != iter.End {
|
||||
t.Errorf("SuperKmer %d: different boundaries: slice=[%d:%d], iter=[%d:%d]",
|
||||
i, slice.Start, slice.End, iter.Start, iter.End)
|
||||
}
|
||||
|
||||
if string(slice.Sequence) != string(iter.Sequence) {
|
||||
t.Errorf("SuperKmer %d: different sequences: slice=%s, iter=%s",
|
||||
i, string(slice.Sequence), string(iter.Sequence))
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// Note: Tests for ToBioSequence and SuperKmerWorker are in a separate
|
||||
// integration test package to avoid circular dependencies between
|
||||
// obikmer and obiseq packages.
|
||||
Reference in New Issue
Block a user