obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Add a first version of obitag the successor of ecotag

Browse Source
This commit is contained in:
Eric Coissac
2022-10-26 13:16:56 +02:00
parent e17d1fbca6
commit 8aa323dad5
17 changed files with 884 additions and 5 deletions
Download Patch File Download Diff File Expand all files Collapse all files

39
pkg/obialign/lcs.go
View File

@ -96,8 +96,18 @@ func (matrix *LCSMatrix) Set(i, j int, score, length int16) {
}
}
// Computes the LCS between two DNA sequences and the length of the
// corresponding alignment
func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
matrix *LCSMatrix) (int, int) {
if seqA.Length() == 0 {
log.Fatal("Sequence A has a length of 0")
}
if seqB.Length() == 0 {
log.Fatal("Sequence B has a length of 0")
}
// swapped := false
if seqA.Length() < seqB.Length() {
@ -105,18 +115,39 @@ func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
// swapped = true
}
if (seqA.Length() - seqB.Length()) > maxError {
return -1, -1
}
matrix = NewLCSMatrix(matrix, seqA.Length(), seqB.Length(), maxError)
la := seqA.Length()
lb := seqB.Length()
sa := seqA.Sequence()
sb := seqB.Sequence()
matrix = NewLCSMatrix(matrix, la, lb, maxError)
for i := 1; i <= matrix.l; i++ {
ij := max(1, i-matrix.extra)
sj := min(i+matrix.delta+matrix.extra, matrix.ll)
for j := ij; j <= sj; j++ {
sd, ld := matrix.Get(i-1, j-1)
if seqB.Sequence()[i-1] == seqA.Sequence()[j-1] {
if i > lb {
log.Println("Error on seq B ", 1, matrix.l)
log.Println(i)
log.Println(seqB.Length(), "/", lb)
log.Println(string(sa))
log.Fatalln(string(sb))
}
if j > la {
log.Println("Error on seq A ", ij, sj)
log.Println(j)
log.Println(seqA.Length(), "/", la)
log.Println(string(sa))
log.Fatalln(string(sb))
}
if sb[i-1] == sa[j-1] {
sd++
}
sup, lup := matrix.Get(i-1, j)
@ -132,11 +163,13 @@ func LCSScore(seqA, seqB *obiseq.BioSequence, maxError int,
}
}
s, l := matrix.Get(seqB.Length(), seqA.Length())
s, l := matrix.Get(lb, la)
if (l - s) > int16(maxError) {
// log.Println(l,s,l-s,maxError)
return -1, -1
}
return int(s), int(l)
}