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Add default taxonomy

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This commit is contained in:
Eric Coissac
2024-11-16 10:01:07 +01:00
parent 7633fc4d23
commit f3d8707c08
3 changed files with 66 additions and 11 deletions
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13
cmd/obitools/obifind/main.go
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@ -5,6 +5,7 @@ import (
"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/obifind"
)
@ -23,12 +24,8 @@ func main() {
switch {
case obifind.CLIRequestsPathForTaxid() != "NA":
taxonomy, err := obifind.CLILoadSelectedTaxonomy()
if err != nil {
fmt.Printf("%+v", err)
}
taxon := taxonomy.Taxon(obifind.CLIRequestsPathForTaxid())
taxon := obitax.DefaultTaxonomy().Taxon(obifind.CLIRequestsPathForTaxid())
if taxon == nil {
fmt.Printf("%+v", err)
@ -44,11 +41,7 @@ func main() {
fmt.Sprintf("path:%s", taxon.String()))
case len(args) == 0:
taxonomy, err := obifind.CLILoadSelectedTaxonomy()
if err != nil {
fmt.Printf("%+v", err)
}
taxonomy := obitax.DefaultTaxonomy()
obifind.TaxonWriter(restrictions(taxonomy.Iterator()), "")
default: