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Change path of the obitools pkg

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Former-commit-id: 311cbf8df3b990b393c6f4885d62e74564423b65
This commit is contained in:
Eric Coissac
2023-11-29 12:14:37 +01:00
parent 72ad84c2d4
commit 8d77cc4133
122 changed files with 1004 additions and 544 deletions
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184
cmd/test/main.go
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@ -1,178 +1,38 @@
package main
import (
"fmt"
"log"
"os"
"runtime/trace"
"cloudeng.io/algo/lcs"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
)
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() {
optionParser := obioptions.GenerateOptionParser(obiconvert.OptionSet)
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
// Creating a file called cpu.trace.
ftrace, err := os.Create("cpu.trace")
if err != nil {
log.Fatal(err)
}
trace.Start(ftrace)
defer trace.Stop()
// "---CACGATCGTGC-CAGTCAT-GGCTAT"
// "CCCCA-GATCGTGCG-AGTCATGGGCTAT"
// 00 0 00000000 1111111 111222
// 01 2 34567889 0123456 789012
// "CA-C-GATCGTGC-CAGTCAT-GGCTAT"
// "CCCCAGATCGTGCG-AGTCATGGGCTAT"
//A := "CACGATCGTGCCCCCAGTCATGGCTAT"
A := "AAATGCCCCAGATCGTGC"
B := "TGCCCCAGAT"
//A = "aaaggaacttggactgaagatttccacagaggttgcgaatgaaaaacacgtattcgaatgcctcaaatacggaatcgatcttgtctg"
A = "aaaggaacttggactgaagatttccacagaggttgcgaatgaaaaacacgtattcgaatgcctcaaatacggaatcgatcttgtctg"
B = "atccggttttacgaaaatgcgtgtggtaggggcttatgaaaacgataatcgaataaaaaagggtaggtgcagagactcaacggaagatgttctaacaaatgg"
// A = "aataa"
// B = "ttttt"
sA := obiseq.NewBioSequence("A", []byte(A), "")
sB := obiseq.NewBioSequence("A", []byte(B), "")
var x interface{}
x = sA
if _, ok := x.(*obiseq.BioSequence); ok {
fmt.Println("Purée")
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
if _, ok := x.(interface{ Length() int }); ok {
fmt.Println("Victoire")
}
frags := obiiter.IFragments(
1000,
100,
10,
100,
obioptions.CLIParallelWorkers(),
)
fmt.Println(goutils.Len(x),goutils.Len([]int{1,2,3}))
// 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.Len(), nil)
fmt.Println(nlcs, nali)
obiconvert.CLIWriteBioSequences(fs.Pipe(frags), true)
// option_parser := obioptions.GenerateOptionParser(
// obiconvert.InputOptionSet,
// )
obiiter.WaitForLastPipe()
// _, args, _ := option_parser(os.Args)
// fs, _ := obiconvert.ReadBioSequencesBatch(args...)
// obiclean.IOBIClean(fs)
// buffer := make([]byte, 0)
// fs.Next()
// s := fs.Get()
// index := obikmer.Index4mer(s, nil, nil)
// for fs.Next() {
// s := fs.Get()
// if s.IsNil() {
// log.Panicln("Read sequence is nil")
// }
// maxshift, maxcount := obikmer.FastShiftFourMer(index, s, buffer)
// fmt.Printf("Shift : %d Score : %d\n", maxshift, maxcount)
// }
// A := []byte("ccgcctccttagaacaggctcctctagaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
// B := []byte("ccgcctccttagaacaggctcctctagaaaaaccatgtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
// B := []byte("cgccaccaccgagatctacactctttccctacacgacgctcttccgatctccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg")
// sA := obiseq.NewBioSequence("A", A, "")
// sB := obiseq.MakeBioSequence("B", B, "")
// s, l := obialign.LCSScore(sA, &sB, 2, nil)
// fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
// s, l = obialign.LCSScore(&sB, &sB, 2, nil)
// fmt.Printf("score : %d length : %d error : %d\n", s, l, l-s)
// 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))
// }
}