mirror of
https://github.com/metabarcoding/obitools4.git
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A fiirst version of LCS score function
This commit is contained in:
1071
LICENCE-CECILL-2.1.txt
Normal file
1071
LICENCE-CECILL-2.1.txt
Normal file
File diff suppressed because it is too large
Load Diff
@ -6,9 +6,9 @@ import (
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"os"
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"runtime/trace"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
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)
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func main() {
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@ -41,29 +41,38 @@ func main() {
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// fmt.Printf("Shift : %d Score : %d\n", maxshift, maxcount)
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// }
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A := []byte("ccgcctccttagaacaggctcctctagaaaaccatagtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
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A := []byte("ccgcctccttagaacaggctcctctagaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
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B := []byte("ccgcctccttagaacaggctcctctagaaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
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// B := []byte("cgccaccaccgagatctacactctttccctacacgacgctcttccgatctccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg")
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sA := obiseq.NewBioSequence("A", A, "")
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// sB := obiseq.MakeBioSequence("B", B, "")
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sB := obiseq.MakeBioSequence("B", B, "")
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pat, _ := obiapat.MakeApatPattern("TCCTTCCAACAGGCTCCTC", 3)
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as, _ := obiapat.MakeApatSequence(sA, false)
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fmt.Println(pat.FindAllIndex(as))
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s, l := obialign.LCSScore(sA, &sB, 2, nil)
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file, _ := os.Open("sample/wolf_diet_ngsfilter.txt")
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xxx, _ := obiformats.ReadNGSFilter(file)
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xxx.Compile(2)
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fmt.Printf("%v\n==================\n", xxx)
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fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
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for pp, m := range xxx {
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fmt.Printf("%v %v\n", pp, *m)
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}
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seqfile, _ := obiformats.ReadFastSeqFromFile("xxxx.fastq")
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for seqfile.Next() {
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seq := seqfile.Get()
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barcode, _ := xxx.ExtractBarcode(seq, true)
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fmt.Println(obiformats.FormatFasta(barcode, obiformats.FormatFastSeqOBIHeader))
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}
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s, l = obialign.LCSScore(&sB, &sB, 2, nil)
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fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
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// pat, _ := obiapat.MakeApatPattern("TCCTTCCAACAGGCTCCTC", 3)
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// as, _ := obiapat.MakeApatSequence(sA, false)
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// fmt.Println(pat.FindAllIndex(as))
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// file, _ := os.Open("sample/wolf_diet_ngsfilter.txt")
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// xxx, _ := obiformats.ReadNGSFilter(file)
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// xxx.Compile(2)
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// fmt.Printf("%v\n==================\n", xxx)
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// for pp, m := range xxx {
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// fmt.Printf("%v %v\n", pp, *m)
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// }
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// seqfile, _ := obiformats.ReadFastSeqFromFile("xxxx.fastq")
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// for seqfile.Next() {
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// seq := seqfile.Get()
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// barcode, _ := xxx.ExtractBarcode(seq, true)
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// fmt.Println(obiformats.FormatFasta(barcode, obiformats.FormatFastSeqOBIHeader))
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// }
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}
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142
pkg/obialign/lcs.go
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142
pkg/obialign/lcs.go
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@ -0,0 +1,142 @@
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package obialign
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import (
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"log"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
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)
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func max(a, b int) int {
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if a > b {
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return a
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}
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return b
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}
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func min(a, b int) int {
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if a < b {
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return a
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}
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return b
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}
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type LCSMatrix struct {
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matrix []int16 // Score matrix
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lenght []int16 // Alignment length matrix
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ll int // Length of the longest sequence
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l int // Length of the shortest sequence
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delta int // ll - l
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extra int
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w int
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}
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func NewLCSMatrix(matrix *LCSMatrix, L, l int, maxError int) *LCSMatrix {
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if matrix == nil {
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matrix = &LCSMatrix{}
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}
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if l > L {
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log.Panicf("L (%d) must be greater or equal to l (%d)", L, l)
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}
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delta := L - l
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extra := ((maxError - delta) / 2) + 1
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needed := L * (1 + delta + 2*extra)
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if needed > matrix.Cap() {
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matrix.matrix = make([]int16, needed)
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matrix.lenght = make([]int16, needed)
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}
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matrix.matrix = matrix.matrix[:needed]
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matrix.lenght = matrix.lenght[:needed]
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matrix.ll = L
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matrix.l = l
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matrix.delta = delta
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matrix.extra = extra
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matrix.w = delta + 1 + 2*extra
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return matrix
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}
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func (matrix *LCSMatrix) Cap() int {
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return cap(matrix.matrix)
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}
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func (matrix *LCSMatrix) Length() int {
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return len(matrix.matrix)
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}
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func (matrix *LCSMatrix) Get(i, j int) (int16, int16) {
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ij := max(0, i-matrix.extra)
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sj := min(i+matrix.delta+matrix.extra, matrix.ll)
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switch {
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case i == 0:
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return int16(0), int16(j)
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case j == 0:
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return int16(0), int16(i)
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case j < ij || j > sj:
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return -1, 30000
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default:
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return matrix.matrix[matrix.extra+matrix.w*(i-1)+(matrix.w-1)*(j-i)],
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matrix.lenght[matrix.extra+matrix.w*(i-1)+(matrix.w-1)*(j-i)]
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}
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}
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func (matrix *LCSMatrix) Set(i, j int, score, length int16) {
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ij := max(0, i-matrix.extra)
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sj := min(i+matrix.delta+matrix.extra, matrix.ll)
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if i > 0 && j > 0 && j >= ij && j <= sj {
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matrix.matrix[matrix.extra+matrix.w*(i-1)+(matrix.w-1)*(j-i)] = score
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matrix.lenght[matrix.extra+matrix.w*(i-1)+(matrix.w-1)*(j-i)] = length
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}
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}
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func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
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matrix *LCSMatrix) (int, int) {
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// swapped := false
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if seqA.Length() < seqB.Length() {
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seqA, seqB = seqB, seqA
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// swapped = true
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}
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if (seqA.Length() - seqB.Length()) > maxError {
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return -1, -1
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}
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matrix = NewLCSMatrix(matrix, seqA.Length(), seqB.Length(), maxError)
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for i := 1; i <= matrix.l; i++ {
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ij := max(1, i-matrix.extra)
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sj := min(i+matrix.delta+matrix.extra, matrix.ll)
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for j := ij; j <= sj; j++ {
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sd, ld := matrix.Get(i-1, j-1)
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if seqB.Sequence()[i-1] == seqA.Sequence()[j-1] {
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sd++
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}
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sup, lup := matrix.Get(i-1, j)
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sleft, lleft := matrix.Get(i, j-1)
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switch {
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case sd >= sup && sd >= sleft:
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matrix.Set(i, j, sd, ld+1)
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case sup >= sleft && sup >= sd:
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matrix.Set(i, j, sup, lup+1)
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default:
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matrix.Set(i, j, sleft, lleft+1)
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}
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}
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}
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s, l := matrix.Get(seqB.Length(), seqA.Length())
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if (l - s) > int16(maxError) {
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return -1, -1
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}
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return int(s), int(l)
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}
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