obitools/obitools4
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Every small changes to include into Release 4.0.4

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Former-commit-id: b2a48c5b5c471f072785e02d4bb0f149a09cdf6f
This commit is contained in:
Eric Coissac
2023-08-27 17:22:51 +02:00
parent d437fba535
commit 45ea4dacf7
6 changed files with 82 additions and 23 deletions
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32
cmd/obitools/obilandmark/main.go Normal file
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@ -0,0 +1,32 @@
package main
import (
"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/obilandmark"
"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
)
func main() {
optionParser := obioptions.GenerateOptionParser(obilandmark.OptionSet)
_, args := optionParser(os.Args)
fs, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Errorf("Cannot open file (%v)", err)
os.Exit(1)
}
indexed := obilandmark.CLISelectLandmarkSequences(fs)
obiconvert.CLIWriteBioSequences(indexed, true)
obiiter.WaitForLastPipe()
}

7
cmd/obitools/obitag/main.go
View File

@ -53,8 +53,13 @@ func main() {
references := obitag.CLIRefDB()
var identified obiiter.IBioSequence
identified := obitag.CLIAssignTaxonomy(fs,references,taxo)
if obitag.CLIGeometricMode() {
identified = obitag.CLIGeomAssignTaxonomy(fs, references, taxo)
} else {
identified = obitag.CLIAssignTaxonomy(fs, references, taxo)
}
obiconvert.CLIWriteBioSequences(identified, true)
obiiter.WaitForLastPipe()