First commit

cmd/test/main.go

@@ -0,0 +1,62 @@
+package main
+
+import (
+	"fmt"
+	"log"
+	"os"
+	"runtime/trace"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obialign"
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func main() {
+
+	ftrace, err := os.Create("cpu.trace")
+	if err != nil {
+		log.Fatal(err)
+	}
+	trace.Start(ftrace)
+	defer trace.Stop()
+
+	// option_parser := obioptions.GenerateOptionParser(
+	// 	obiconvert.InputOptionSet,
+	// )
+
+	//_, args, _ := option_parser(os.Args)
+
+	// fs, _ := obiconvert.ReadBioSequences(args...)
+	// 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("ccgcctccttagaacaggctcctctagaaaaccatagtgggatatctaaagaaggcggagatagaaagagcggttcagcaggaatgccgagatggacggcgtgtgacg")
+	B := []byte("cgccaccaccgagatctacactctttccctacacgacgctcttccgatctccgcctccttagaacaggctcctctagaaaagcatagtggggtatctaaaggaggcgg")
+	sA := obiseq.MakeBioSequence("A", A, "")
+	sB := obiseq.MakeBioSequence("B", B, "")
+
+	fmt.Println(string(sA.Sequence()))
+	fmt.Println(sA.Qualities())
+	fmt.Println(string(sB.Sequence()))
+	fmt.Println(sB.Qualities())
+
+	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)
+
+	fmt.Println(string(sA.Sequence()))
+	sA.ReverseComplement(true)
+	fmt.Println(string(sA.Sequence()))
+	fmt.Println(string(sA.Id()))
+}

cmd/test/test_test.go

@@ -0,0 +1,58 @@
+package main_test
+
+import (
+	"fmt"
+	"testing"
+
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiannot"
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiformats"
+	"git.metabarcoding.org/lecasofts/go/oa2/pkg/obiseq"
+)
+
+func TestParseOBIFasta(t *testing.T) {
+	f := "/Users/coissac/travail/Adeline/Soumission_data/Zonation/euka03/euka03.ecotag.fasta.gz"
+
+	var nseq, nread int
+	nseq = 0
+	nread = 0
+
+	fs := obiformats.ReaderFromIlluminaFile(f)
+
+	fmt.Println(f)
+
+	for i := range obiannot.ExtractHeaderChannel(fs, fastseq.ParseOBIHeader) {
+		for _, s := range i {
+			nseq++
+			nread += s.Count()
+		}
+	}
+	fmt.Println(nseq, nread)
+
+}
+
+func ExtractHeaderChannel(fs fastseq.IFastSeq, sequence func(sequence obiseq.Sequence)) {
+	panic("unimplemented")
+}
+
+// Performance test of an ADEXP message parsing
+func BenchmarkParseOBIFasta(t *testing.B) {
+
+	f := "/Users/coissac/travail/Adeline/Soumission_data/Zonation/euka03/euka03.ecotag.fasta.gz"
+
+	var nseq, nread int
+	nseq = 0
+	nread = 0
+
+	fs := fastseq.ReaderFromIlluminaFile(f)
+
+	fmt.Println(f)
+
+	for i := range obiannot.ExtractHeaderChannel(fs, fastseq.ParseOBIHeader) {
+		for _, s := range i {
+			nseq++
+			nread += s.Count()
+		}
+	}
+	fmt.Println(nseq, nread)
+
+}