Patch a bug in the embl reader and adds some doc

Former-commit-id: 9b5f75fb14bcc3043da1647055279987a295d271

pkg/obitax/bioseq_classifier.go

@@ -0,0 +1,64 @@
+package obitax
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
+	log "github.com/sirupsen/logrus"
+)
+
+// TaxonomyClassifier is a function that creates a new instance of the BioSequenceClassifier
+// for taxonomic classification based on a given taxonomic rank, taxonomy, and abort flag.
+//
+// Parameters:
+// - taxonomicRank: the taxonomic rank to classify the sequences at.
+// - taxonomy: the taxonomy object used for classification.
+// - abortOnMissing: a flag indicating whether to abort if a taxon is missing in the taxonomy.
+//
+// Return:
+// - *obiseq.BioSequenceClassifier: the new instance of the BioSequenceClassifier.
+func TaxonomyClassifier(taxonomicRank string,
+	taxonomy *Taxonomy,
+	abortOnMissing bool) *obiseq.BioSequenceClassifier {
+
+	code := func(sequence *obiseq.BioSequence) int {
+		taxid := sequence.Taxid()
+		taxon, err := taxonomy.Taxon(taxid)
+		if err == nil {
+			taxon = taxon.TaxonAtRank(taxonomicRank)
+		} else {
+			taxon = nil
+		}
+		if taxon == nil {
+			if abortOnMissing {
+				if err != nil {
+					log.Fatalf("Taxid %d not found in taxonomy", taxid)
+				} else {
+					log.Fatalf("Taxon at rank %s not found in taxonomy for taxid %d", taxonomicRank, taxid)
+				}
+
+			}
+
+			return 0
+		}
+		return taxon.Taxid()
+	}
+
+	value := func(k int) string {
+		taxon, _ := taxonomy.Taxon(k)
+		return taxon.ScientificName()
+	}
+
+	reset := func() {
+	}
+
+	clone := func() *obiseq.BioSequenceClassifier {
+		return TaxonomyClassifier(taxonomicRank, taxonomy, abortOnMissing)
+	}
+
+	c := obiseq.BioSequenceClassifier{
+		Code:  code,
+		Value: value,
+		Reset: reset,
+		Clone: clone,
+		Type:  "TaxonomyClassifier"}
+	return &c
+}