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A fiirst version of LCS score function

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This commit is contained in:
Eric Coissac
2022-03-07 16:37:21 +01:00
parent 62cd1c44dc
commit 656eda1f73
3 changed files with 1242 additions and 20 deletions
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49
cmd/test/main.go
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@ -6,9 +6,9 @@ import (
"os"
"runtime/trace"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
)
func main() {
@ -41,29 +41,38 @@ func main() {
// fmt.Printf("Shift : %d Score : %d\n", maxshift, maxcount)
// }
A := []byte("ccgcctccttagaacaggctcctctagaaaaccatagtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
A := []byte("ccgcctccttagaacaggctcctctagaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
B := []byte("ccgcctccttagaacaggctcctctagaaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
// B := []byte("cgccaccaccgagatctacactctttccctacacgacgctcttccgatctccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg")
sA := obiseq.NewBioSequence("A", A, "")
// sB := obiseq.MakeBioSequence("B", B, "")
sB := obiseq.MakeBioSequence("B", B, "")
pat, _ := obiapat.MakeApatPattern("TCCTTCCAACAGGCTCCTC", 3)
as, _ := obiapat.MakeApatSequence(sA, false)
fmt.Println(pat.FindAllIndex(as))
s, l := obialign.LCSScore(sA, &sB, 2, nil)
file, _ := os.Open("sample/wolf_diet_ngsfilter.txt")
xxx, _ := obiformats.ReadNGSFilter(file)
xxx.Compile(2)
fmt.Printf("%v\n==================\n", xxx)
fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
for pp, m := range xxx {
fmt.Printf("%v %v\n", pp, *m)
}
s, l = obialign.LCSScore(&sB, &sB, 2, nil)
seqfile, _ := obiformats.ReadFastSeqFromFile("xxxx.fastq")
fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
for seqfile.Next() {
seq := seqfile.Get()
barcode, _ := xxx.ExtractBarcode(seq, true)
fmt.Println(obiformats.FormatFasta(barcode, obiformats.FormatFastSeqOBIHeader))
}
// pat, _ := obiapat.MakeApatPattern("TCCTTCCAACAGGCTCCTC", 3)
// as, _ := obiapat.MakeApatSequence(sA, false)
// fmt.Println(pat.FindAllIndex(as))
// file, _ := os.Open("sample/wolf_diet_ngsfilter.txt")
// xxx, _ := obiformats.ReadNGSFilter(file)
// xxx.Compile(2)
// fmt.Printf("%v\n==================\n", xxx)
// for pp, m := range xxx {
// fmt.Printf("%v %v\n", pp, *m)
// }
// seqfile, _ := obiformats.ReadFastSeqFromFile("xxxx.fastq")
// for seqfile.Next() {
// seq := seqfile.Get()
// barcode, _ := xxx.ExtractBarcode(seq, true)
// fmt.Println(obiformats.FormatFasta(barcode, obiformats.FormatFastSeqOBIHeader))
// }
}