obitools/obitools4
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correction in obitag to save partially indexed reference db

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Former-commit-id: ba1e5ce42ac77b143d20fd8903a6e157d83c09f5
This commit is contained in:
Eric Coissac
2023-06-07 17:48:38 +02:00
parent 63dc67f344
commit 49fa1a76cb
1 changed files with 17 additions and 2 deletions
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19
cmd/obitools/obitag/main.go
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@ -3,10 +3,12 @@ package main
import (
"fmt"
"os"
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiiter"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obitag"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
@ -30,6 +32,9 @@ func main() {
// trace.Start(ftrace)
// defer trace.Stop()
obioptions.SetWorkerPerCore(2)
obioptions.SetReadWorkerPerCore(0.5)
optionParser := obioptions.GenerateOptionParser(obitag.OptionSet)
_, args := optionParser(os.Args)
@ -37,14 +42,24 @@ func main() {
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)",err)
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
identified := obitag.AssignTaxonomy(fs)
taxo, error := obifind.CLILoadSelectedTaxonomy()
if error != nil {
log.Panicln(error)
}
references := obitag.CLIRefDB()
identified := obitag.CLIAssignTaxonomy(fs,references,taxo)
obiconvert.CLIWriteBioSequences(identified, true)
obiiter.WaitForLastPipe()
obitag.CLISaveRefetenceDB(references)
fmt.Println("")
}