mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
70 lines
1.8 KiB
Go
70 lines
1.8 KiB
Go
package main
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import (
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"fmt"
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"log"
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"os"
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"runtime/trace"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiapat"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiformats"
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
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)
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func main() {
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ftrace, err := os.Create("cpu.trace")
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if err != nil {
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log.Fatal(err)
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}
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trace.Start(ftrace)
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defer trace.Stop()
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// option_parser := obioptions.GenerateOptionParser(
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// obiconvert.InputOptionSet,
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// )
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//_, args, _ := option_parser(os.Args)
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// fs, _ := obiconvert.ReadBioSequences(args...)
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// buffer := make([]byte, 0)
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// fs.Next()
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// s := fs.Get()
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// index := obikmer.Index4mer(s, nil, nil)
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// for fs.Next() {
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// s := fs.Get()
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// if s.IsNil() {
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// log.Panicln("Read sequence is nil")
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// }
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// maxshift, maxcount := obikmer.FastShiftFourMer(index, s, buffer)
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// fmt.Printf("Shift : %d Score : %d\n", maxshift, maxcount)
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// }
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A := []byte("ccgcctccttagaacaggctcctctagaaaaccatagtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
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// B := []byte("cgccaccaccgagatctacactctttccctacacgacgctcttccgatctccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg")
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sA := obiseq.NewBioSequence("A", A, "")
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// sB := obiseq.MakeBioSequence("B", B, "")
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pat, _ := obiapat.MakeApatPattern("TCCTTCCAACAGGCTCCTC", 3)
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as, _ := obiapat.MakeApatSequence(sA, false)
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fmt.Println(pat.FindAllIndex(as))
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file, _ := os.Open("sample/wolf_diet_ngsfilter.txt")
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xxx, _ := obiformats.ReadNGSFilter(file)
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xxx.Compile(2)
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fmt.Printf("%v\n==================\n", xxx)
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for pp, m := range xxx {
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fmt.Printf("%v %v\n", pp, *m)
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}
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seqfile, _ := obiformats.ReadFastSeqFromFile("xxxx.fastq")
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for seqfile.Next() {
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seq := seqfile.Get()
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barcode, _ := xxx.ExtractBarcode(seq, true)
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fmt.Println(obiformats.FormatFasta(barcode, obiformats.FormatFastSeqOBIHeader))
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}
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}
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