First prelease of obiannotate

cmd/obitools/obiannotate/main.go

@@ -0,0 +1,42 @@
+package main
+
+import (
+	"os"
+	"runtime/pprof"
+
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiannotate"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+)
+
+func main() {
+
+	defer obiseq.LogBioSeqStatus()
+
+	// go tool pprof -http=":8000" ./obipairing ./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()
+
+	optionParser := obioptions.GenerateOptionParser(obiannotate.OptionSet)
+
+	_, args, _ := optionParser(os.Args)
+
+	sequences, _ := obiconvert.ReadBioSequences(args...)
+	annotator := obiannotate.CLIAnnotationPipeline()
+	obiconvert.WriteBioSequences(sequences.Pipe(annotator), true)
+}