Changes to be committed:

modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitag2/main.go
	modified:   go.mod
	modified:   go.sum
	modified:   pkg/obiformats/ncbitaxdump/read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/attributes.go
	modified:   pkg/obiseq/taxonomy_lca.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obiseq/taxonomy_predicate.go
	modified:   pkg/obitax/inner.go
	modified:   pkg/obitax/lca.go
	new file:   pkg/obitax/taxid.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obicleandb/obicleandb.go
	modified:   pkg/obitools/obigrep/options.go
	modified:   pkg/obitools/obilandmark/obilandmark.go
	modified:   pkg/obitools/obilandmark/options.go
	modified:   pkg/obitools/obirefidx/famlilyindexing.go
	modified:   pkg/obitools/obirefidx/geomindexing.go
	modified:   pkg/obitools/obirefidx/obirefidx.go
	modified:   pkg/obitools/obirefidx/options.go
	modified:   pkg/obitools/obitag/obigeomtag.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitag/options.go
	modified:   pkg/obiutils/strings.go

pkg/obiseq/attributes.go

@@ -389,18 +389,6 @@ func (s *BioSequence) SetCount(count int) {
 	s.SetAttribute("count", count)
 }
 
-// SetTaxid sets the taxid for the BioSequence.
-//
-// Parameters:
-//
-//	taxid - the taxid to set.
-func (s *BioSequence) SetTaxid(taxid string) {
-	if taxid == "" {
-		taxid = "NA"
-	}
-	s.SetAttribute("taxid", taxid)
-}
-
 func (s *BioSequence) OBITagRefIndex(slot ...string) map[int]string {
 	key := "obitag_ref_index"
 

pkg/obiseq/taxonomy_lca.go

@@ -123,7 +123,6 @@ func AddLCAWorker(taxonomy *obitax.Taxonomy, slot_name string, threshold float64
 		sequence.SetAttribute(slot_name, lca.String())
 		sequence.SetAttribute(lca_name, lca.ScientificName())
 		sequence.SetAttribute(lca_error, math.Round((1-rans)*1000)/1000)
-
 		return BioSequenceSlice{sequence}, nil
 	}
 

pkg/obiseq/taxonomy_methods.go

@@ -1,6 +1,10 @@
 package obiseq
 
 import (
+	"fmt"
+
+	log "github.com/sirupsen/logrus"
+
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 )
 
@@ -12,6 +16,23 @@ func (s *BioSequence) Taxon(taxonomy *obitax.Taxonomy) *obitax.Taxon {
 	return taxonomy.Taxon(taxid)
 }
 
+// SetTaxid sets the taxid for the BioSequence.
+//
+// Parameters:
+//
+//	taxid - the taxid to set.
+func (s *BioSequence) SetTaxid(taxid string) {
+	if taxid == "" {
+		taxid = "NA"
+	}
+	s.SetAttribute("taxid", taxid)
+}
+
+func (s *BioSequence) SetTaxon(taxon *obitax.Taxon) {
+	taxid := taxon.String()
+	s.SetTaxid(taxid)
+}
+
 // Taxid returns the taxonomic ID associated with the BioSequence.
 //
 // It retrieves the "taxid" attribute from the BioSequence's attributes map.
@@ -25,7 +46,20 @@ func (s *BioSequence) Taxid() (taxid string) {
 		taxid = s.taxon.String()
 		ok = true
 	} else {
-		taxid, ok = s.GetStringAttribute("taxid")
+		var ta interface{}
+		ta, ok = s.GetAttribute("taxid")
+		if ok {
+			switch tv := ta.(type) {
+			case string:
+				taxid = tv
+			case int:
+				taxid = fmt.Sprintf("%d", tv)
+			case float64:
+				taxid = fmt.Sprintf("%d", int(tv))
+			default:
+				log.Fatalf("Taxid: %v is not a string or an integer (%T)", ta, ta)
+			}
+		}
 	}
 
 	if !ok {

pkg/obiseq/taxonomy_predicate.go

@@ -47,14 +47,7 @@ func IsAValidTaxon(taxonomy *obitax.Taxonomy, withAutoCorrection ...bool) Sequen
 
 // A function that takes a taxonomy and a taxid as arguments and returns a function that takes a
 // pointer to a BioSequence as an argument and returns a boolean.
-func IsSubCladeOf(taxonomy *obitax.Taxonomy, taxid string) SequencePredicate {
-	parent := taxonomy.Taxon(taxid)
-
-	if parent == nil {
-		log.Fatalf("Cannot find taxon : %s in taxonomy %s",
-			taxid,
-			taxonomy.Name())
-	}
+func IsSubCladeOf(taxonomy *obitax.Taxonomy, parent *obitax.Taxon) SequencePredicate {
 
 	f := func(sequence *BioSequence) bool {
 		taxon := sequence.Taxon(taxonomy)