Refactor primer logic and enhance taxonomy features

This commit introduces refinements to primer design strategies, species identification rules, and performance analysis. It also updates taxonomy handling by implementing methods for setting and dropping taxonomic paths, along with necessary utility improvements for set handling and comprehensive test coverage.

pkg/obiseq/taxonomy_methods.go

@@ -176,6 +176,10 @@ func (sequence *BioSequence) SetFamily(taxonomy *obitax.Taxonomy) *obitax.Taxon
 	return sequence.SetTaxonAtRank(taxonomy, "family")
 }
 
+// TaxonomicPathAttribute is the attribute holding the taxonomic path of a
+// sequence, from the root to its taxon (see obiannotate --taxonomic-path).
+const TaxonomicPathAttribute = "taxonomic_path"
+
 func (sequence *BioSequence) SetPath(taxonomy *obitax.Taxonomy) []string {
 	taxon := sequence.Taxon(taxonomy)
 	path := taxon.Path()
@@ -186,13 +190,13 @@ func (sequence *BioSequence) SetPath(taxonomy *obitax.Taxonomy) []string {
 		spath[lpath-i] = path.Get(i).FullString(taxonomy.Code())
 	}
 
-	sequence.SetAttribute("taxonomic_path", spath)
+	sequence.SetAttribute(TaxonomicPathAttribute, spath)
 
 	return spath
 }
 
 func (sequence *BioSequence) Path() []string {
-	path, ok := sequence.GetAttribute("taxonomic_path")
+	path, ok := sequence.GetAttribute(TaxonomicPathAttribute)
 
 	if !ok {
 		if taxo := obitax.DefaultTaxonomy(); taxo != nil {