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

Adds a reader for NGS filter files and change some API for the apat library

Browse Source
This commit is contained in:
Eric Coissac
2022-01-18 13:09:32 +01:00
parent 6571296bb2
commit 4551df08b1
13 changed files with 301 additions and 96 deletions
Download Patch File Download Diff File Expand all files Collapse all files

29
cmd/test/main.go
View File

@ -6,7 +6,8 @@ import (
"os"
"runtime/trace"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obialign"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
)
@ -41,27 +42,17 @@ func main() {
// }
A := []byte("ccgcctccttagaacaggctcctctagaaaaccatagtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
B := []byte("cgccaccaccgagatctacactctttccctacacgacgctcttccgatctccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg")
// B := []byte("cgccaccaccgagatctacactctttccctacacgacgctcttccgatctccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg")
sA := obiseq.MakeBioSequence("A", A, "")
sB := obiseq.MakeBioSequence("B", B, "")
// sB := obiseq.MakeBioSequence("B", B, "")
fmt.Println(string(sA.Sequence()))
fmt.Println(sA.Qualities())
fmt.Println(string(sB.Sequence()))
fmt.Println(sB.Qualities())
pat, _ := obiapat.MakeApatPattern("TCCTTCCAACAGGCTCCTC", 3)
as, _ := obiapat.MakeApatSequence(sA, false)
fmt.Println(pat.FindAllIndex(as))
score, path := obialign.PELeftAlign(sA, sB, 2, obialign.NilPEAlignArena)
fmt.Printf("Score : %d Path : %v\n", score, path)
score, path = obialign.PERightAlign(sA, sB, 2, obialign.NilPEAlignArena)
fmt.Printf("Score : %d Path : %v\n", score, path)
file, _ := os.Open("sample/wolf_diet_ngsfilter.txt")
xxx, _ := obiformats.ReadNGSFilter(file)
fmt.Println(string(sA.Sequence()))
sA.ReverseComplement(true)
fmt.Println(string(sA.Sequence()))
fmt.Println(string(sA.Id()))
sA.Reset()
fmt.Println(sA.Length())
fmt.Println(sA.String())
fmt.Println(xxx)
}