From 49fa1a76cbc5fbafdff078f0f0536d993d7462bc Mon Sep 17 00:00:00 2001 From: Eric Coissac Date: Wed, 7 Jun 2023 17:48:38 +0200 Subject: [PATCH] correction in obitag to save partially indexed reference db Former-commit-id: ba1e5ce42ac77b143d20fd8903a6e157d83c09f5 --- cmd/obitools/obitag/main.go | 19 +++++++++++++++++-- 1 file changed, 17 insertions(+), 2 deletions(-) diff --git a/cmd/obitools/obitag/main.go b/cmd/obitools/obitag/main.go index b72c2e9..efcc07a 100644 --- a/cmd/obitools/obitag/main.go +++ b/cmd/obitools/obitag/main.go @@ -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("") }