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Adds the obimicrosat command

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This commit is contained in:
Eric Coissac
2024-08-05 15:31:20 +02:00
parent 3f57935328
commit bdb96dda94
11 changed files with 419 additions and 5 deletions
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49
cmd/obitools/obimicrosat/main.go Normal file
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package main
import (
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiiter"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obimicrosat"
)
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(obimicrosat.OptionSet)
_, args := optionParser(os.Args)
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
selected := obimicrosat.CLIAnnotateMicrosat(sequences)
obiconvert.CLIWriteBioSequences(selected, true)
obiiter.WaitForLastPipe()
}