obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

First version of obisplit and patch a bug in the new workers API

Browse Source 
Former-commit-id: f28af9f104c08d68e29fd866739d8dd58241da63
This commit is contained in:
Eric Coissac
2024-03-03 11:16:24 -04:00
parent 0f3871d203
commit 7bd073ccd4
7 changed files with 507 additions and 37 deletions
Download Patch File Download Diff File Expand all files Collapse all files

57
cmd/obitools/obisplit/main.go Normal file
View File

@ -0,0 +1,57 @@
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/obisplit"
)
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(obisplit.OptionSet)
_, args := optionParser(os.Args)
if obisplit.CLIAskConfigTemplate() {
fmt.Print(obisplit.CLIConfigTemplate())
os.Exit(0)
}
sequences, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
annotator := obisplit.CLISlitPipeline()
obiconvert.CLIWriteBioSequences(sequences.Pipe(annotator), true)
obiiter.WaitForLastPipe()
}