obitools/obitools4
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remove the obitag2 command

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This commit is contained in:
Eric Coissac
2025-01-07 11:50:28 +01:00
parent 4fe0db63ff
commit 67c0d00a4d
1 changed files with 0 additions and 61 deletions
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61
cmd/obitools/obitag2/main.go
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@ -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("")
}