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add the --download-ncbi option to obitaxonomy

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This commit is contained in:
Eric Coissac
2025-01-29 12:38:39 +01:00
parent b6b18c0fa1
commit 8a28c9ae7c
5 changed files with 87 additions and 3 deletions
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12
cmd/obitools/obitaxonomy/main.go
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@ -1,13 +1,14 @@
package main
import (
"log"
"os"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitaxonomy"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
log "github.com/sirupsen/logrus"
)
func main() {
@ -19,6 +20,15 @@ func main() {
switch {
case obitaxonomy.CLIDownloadNCBI():
err := obitaxonomy.CLIDownloadNCBITaxdump()
if err != nil {
log.Errorf("Cannot download NCBI taxonomy: %s", err.Error())
os.Exit(1)
}
os.Exit(0)
case obitaxonomy.CLIDumpSubtaxonomy():
iterator = obitaxonomy.CLISubTaxonomyIterator()