diff --git a/cmd/obitools/obitag2/main.go b/cmd/obitools/obitag2/main.go deleted file mode 100644 index dc32e4c..0000000 --- a/cmd/obitools/obitag2/main.go +++ /dev/null @@ -1,61 +0,0 @@ -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/obitax" - "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert" - "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...) - obiconvert.OpenSequenceDataErrorMessage(args, err) - - taxo := obitax.DefaultTaxonomy() - if taxo == nil { - log.Panicln("No loaded taxonomy") - } - - references := obitag.CLIRefDB() - - identified := obitag2.CLIAssignTaxonomy(fs, references, taxo) - - obiconvert.CLIWriteBioSequences(identified, true) - obiiter.WaitForLastPipe() - - fmt.Println("") -}