obitools/obitools4
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first preliminary version of obiscript.

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Former-commit-id: 0d2c0fc5e33e0873ba5c04aca4cf7dd69aa83c90
This commit is contained in:
Eric Coissac
2024-03-06 12:56:44 -03:00
parent b4afd784dc
commit b40015deb7
10 changed files with 739 additions and 4 deletions
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57
cmd/obitools/obiscript/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/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/obiscript"
)
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(obiscript.OptionSet)
_, args := optionParser(os.Args)
if obiscript.CLIAskScriptTemplate() {
fmt.Print(obiscript.CLIScriptTemplate())
os.Exit(0)
}
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
annotator := obiscript.CLIScriptPipeline()
obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)
obiiter.WaitForLastPipe()
}