obitag xprize version

Former-commit-id: 2c47d88724102b115aac5641abccb880dfbec64d

cmd/obitools/obitag2/main.go

@@ -0,0 +1,65 @@
+package main
+
+import (
+	"fmt"
+	"os"
+
+	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/obitools/obifind"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitag"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitag2"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
+)
+
+func main() {
+
+	// go tool pprof -http=":8000" ./build/obitag ./cpu.pprof
+	// f, err := os.Create("cpu.pprof")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// pprof.StartCPUProfile(f)
+	// defer pprof.StopCPUProfile()
+
+	// go tool trace cpu.trace
+	// ftrace, err := os.Create("cpu.trace")
+	// if err != nil {
+	// 	log.Fatal(err)
+	// }
+	// trace.Start(ftrace)
+	// defer trace.Stop()
+
+	obioptions.SetWorkerPerCore(2)
+	obioptions.SetStrictReadWorker(1)
+	obioptions.SetStrictWriteWorker(1)
+	obioptions.SetBatchSize(10)
+
+	optionParser := obioptions.GenerateOptionParser(obitag.OptionSet)
+
+	_, args := optionParser(os.Args)
+
+	fs, err := obiconvert.CLIReadBioSequences(args...)
+
+	if err != nil {
+		log.Errorf("Cannot open file (%v)", err)
+		os.Exit(1)
+	}
+
+	taxo, error := obifind.CLILoadSelectedTaxonomy()
+	if error != nil {
+		log.Panicln(error)
+	}
+
+	references := obitag.CLIRefDB()
+
+	identified := obitag2.CLIAssignTaxonomy(fs, references, taxo)
+
+	obiconvert.CLIWriteBioSequences(identified, true)
+	obiiter.WaitForLastPipe()
+
+	fmt.Println("")
+}