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Patch header parting and formatiing

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This commit is contained in:
Eric Coissac
2022-05-27 11:53:29 +03:00
parent 656eda1f73
commit f14860a486
8 changed files with 91 additions and 29 deletions
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36
cmd/test/main.go
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@ -1,14 +1,13 @@
package main
import (
"fmt"
"log"
"os"
"runtime/trace"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"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"
)
func main() {
@ -20,13 +19,16 @@ func main() {
trace.Start(ftrace)
defer trace.Stop()
// option_parser := obioptions.GenerateOptionParser(
// obiconvert.InputOptionSet,
// )
option_parser := obioptions.GenerateOptionParser(
obiconvert.InputOptionSet,
)
//_, args, _ := option_parser(os.Args)
_, args, _ := option_parser(os.Args)
fs, _ := obiconvert.ReadBioSequencesBatch(args...)
obiclean.IOBIClean(fs)
// fs, _ := obiconvert.ReadBioSequences(args...)
// buffer := make([]byte, 0)
// fs.Next()
// s := fs.Get()
@ -41,19 +43,19 @@ func main() {
// fmt.Printf("Shift : %d Score : %d\n", maxshift, maxcount)
// }
A := []byte("ccgcctccttagaacaggctcctctagaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
B := []byte("ccgcctccttagaacaggctcctctagaaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
// A := []byte("ccgcctccttagaacaggctcctctagaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
// B := []byte("ccgcctccttagaacaggctcctctagaaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
// B := []byte("cgccaccaccgagatctacactctttccctacacgacgctcttccgatctccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg")
sA := obiseq.NewBioSequence("A", A, "")
sB := obiseq.MakeBioSequence("B", B, "")
// sA := obiseq.NewBioSequence("A", A, "")
// sB := obiseq.MakeBioSequence("B", B, "")
s, l := obialign.LCSScore(sA, &sB, 2, nil)
// s, l := obialign.LCSScore(sA, &sB, 2, nil)
fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
// fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
s, l = obialign.LCSScore(&sB, &sB, 2, nil)
// s, l = obialign.LCSScore(&sB, &sB, 2, nil)
fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
// fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
// pat, _ := obiapat.MakeApatPattern("TCCTTCCAACAGGCTCCTC", 3)
// as, _ := obiapat.MakeApatSequence(sA, false)