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New version of LCS computation, with abug on alignment length patched patched

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This commit is contained in:
Eric Coissac
2022-11-15 08:21:46 +01:00
parent 18be4becec
commit 340579f6d7
5 changed files with 238 additions and 383 deletions
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99
cmd/test/main.go
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@ -1,15 +1,65 @@
package main
import (
"fmt"
"log"
"os"
"runtime/trace"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiclean"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"cloudeng.io/algo/lcs"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
func SESStat(script *lcs.EditScript[byte]) (int, int) {
llcs := 0
gaps := 0
extra := 0
i := 0
ls := len(*script)
for i < ls {
e := (*script)[i]
// log.Println(i,e,e.Op)
switch e.Op {
case lcs.Identical: // 2
if gaps > 0 {
extra += gaps
}
llcs++
gaps = 0
i++
case lcs.Delete: // 1
if i+1 < ls {
en := (*script)[i+1]
if en.Op == lcs.Identical && e.Val == en.Val {
log.Println("Swap delete")
(*script)[i], (*script)[i+1] = (*script)[i+1], (*script)[i]
continue
}
}
gaps--
i++
case lcs.Insert: // 0
if i+1 < ls {
en := (*script)[i+1]
if en.Op == lcs.Identical && e.Val == en.Val {
log.Println("Swap Insert")
(*script)[i], (*script)[i+1] = (*script)[i+1], (*script)[i]
continue
}
}
gaps++
i++
}
}
if gaps > 0 {
extra += gaps
}
return llcs, extra
}
func main() {
// Creating a file called cpu.trace.
@ -20,15 +70,46 @@ func main() {
trace.Start(ftrace)
defer trace.Stop()
option_parser := obioptions.GenerateOptionParser(
obiconvert.InputOptionSet,
)
// "---CACGATCGTGC-CAGTCAT-GGCTAT"
// "CCCCA-GATCGTGCG-AGTCATGGGCTAT"
_, args, _ := option_parser(os.Args)
// 00 0 00000000 1111111 111222
// 01 2 34567889 0123456 789012
// "CA-C-GATCGTGC-CAGTCAT-GGCTAT"
// "CCCCAGATCGTGCG-AGTCATGGGCTAT"
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
//A := "CACGATCGTGCCCCCAGTCATGGCTAT"
A := "AAATGCCCCAGATCGTGC"
B := "TGCCCCAGAT"
obiclean.IOBIClean(fs)
//A = "aaaggaacttggactgaagatttccacagaggttgcgaatgaaaaacacgtattcgaatgcctcaaatacggaatcgatcttgtctg"
A = "aaaggaacttggactgaagatttccacagaggttgcgaatgaaaaacacgtattcgaatgcctcaaatacggaatcgatcttgtctg"
B = "atccggttttacgaaaatgcgtgtggtaggggcttatgaaaacgataatcgaataaaaaagggtaggtgcagagactcaacggaagatgttctaacaaatgg"
// A = "aataa"
// B = "ttttt"
sA := obiseq.NewBioSequence("A", []byte(A), "")
sB := obiseq.NewBioSequence("A", []byte(B), "")
// M := lcs.NewMyers([]byte(A), []byte(B))
// fmt.Println(M.LCS())
// fmt.Println(M.SES())
// fmt.Println(len(M.LCS()))
// M.SES().FormatHorizontal(os.Stdout, []byte(B))
// llcs, extra := SESStat(M.SES())
// nlcs, nali := obialign.LCSScore(sA, sB, sB.Length(), nil)
// fmt.Println(llcs, extra, len(A)+extra)
// fmt.Println(nlcs, nali)
nlcs, nali := obialign.FastLCSScore(sA, sB, sB.Length(), nil)
fmt.Println(nlcs, nali)
// option_parser := obioptions.GenerateOptionParser(
// obiconvert.InputOptionSet,
// )
// _, args, _ := option_parser(os.Args)
// fs, _ := obiconvert.ReadBioSequencesBatch(args...)
// obiclean.IOBIClean(fs)
// buffer := make([]byte, 0)
// fs.Next()