obitools/obitools4
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obitag xprize version

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Former-commit-id: 2c47d88724102b115aac5641abccb880dfbec64d
This commit is contained in:
Eric Coissac
2024-07-25 18:11:11 -04:00
parent 67665a6b40
commit 2247c3bc0a
1 changed files with 65 additions and 0 deletions
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cmd/obitools/obitag2/main.go Normal file
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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("")
}