Debug on taxonomy extraction and CSV conversion

pkg/obiformats/options.go

@@ -44,6 +44,7 @@ type __options__ struct {
 	with_scientific_name  bool
 	without_root_path     bool
 	raw_taxid             bool
+	u_to_t                bool
 	with_metadata         []string
 }
 
@@ -88,6 +89,7 @@ func MakeOptions(setters []WithOption) Options {
 		with_path:             false,
 		with_rank:             true,
 		with_taxid:            true,
+		u_to_t:                false,
 		with_scientific_name:  false,
 		without_root_path:     false,
 		raw_taxid:             false,
@@ -263,6 +265,10 @@ func (o *Options) RawTaxid() bool {
 	return o.pointer.raw_taxid
 }
 
+func (o *Options) UtoT() bool {
+	return o.pointer.u_to_t
+}
+
 // WithMetadata returns a slice of strings containing the metadata
 // associated with the Options instance. It retrieves the metadata
 // from the pointer's with_metadata field.
@@ -598,6 +604,14 @@ func OptionsRawTaxid(value bool) WithOption {
 	return f
 }
 
+func OptionsUtoT(value bool) WithOption {
+	f := WithOption(func(opt Options) {
+		opt.pointer.u_to_t = value
+	})
+
+	return f
+}
+
 func OptionsWithMetadata(values ...string) WithOption {
 	f := WithOption(func(opt Options) {
 		opt.pointer.with_metadata = values

pkg/obiiter/extract_taxonomy.go

@@ -2,17 +2,24 @@ package obiiter
 
 import "git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 
+// ExtractTaxonomy iterates over each slice of the IBioSequence and extracts the taxonomy from it using the ExtractTaxonomy method of the slice.
+// If the seqAsTaxa parameter is true, then the sequence itself will be treated as a single taxon. Otherwise, each element in the slice will be treated separately.
+// The function returns an error if any of the ExtractTaxonomy calls fail and nil otherwise.
 func (iterator *IBioSequence) ExtractTaxonomy(seqAsTaxa bool) (taxonomy *obitax.Taxonomy, err error) {
-
+	// Iterate over each slice in the iterator
 	for iterator.Next() {
+		// Get the current slice
 		slice := iterator.Get().Slice()
 
+		// Try to extract taxonomy from the slice
 		taxonomy, err = slice.ExtractTaxonomy(taxonomy, seqAsTaxa)
 
+		// If an error occurred during extraction, return it immediately
 		if err != nil {
 			return
 		}
 	}
 
+	// Return the extracted taxonomy and no error if all slices were successfully processed
 	return
 }

pkg/obioptions/version.go

@@ -8,7 +8,7 @@ import (
 // corresponds to the last commit, and not the one when the file will be
 // commited
 
-var _Commit = "27fa984"
+var _Commit = "235a7e2"
 var _Version = "Release 4.4.0"
 
 // Version returns the version of the obitools package.

pkg/obitax/default_taxonomy.go

@@ -26,7 +26,7 @@ func (taxonomy *Taxonomy) OrDefault(panicOnNil bool) *Taxonomy {
 	return taxonomy
 }
 
-func IsDefaultTaxonomyDefined() bool {
+func HasDefaultTaxonomyDefined() bool {
 	return __defaut_taxonomy__ != nil
 }
 

pkg/obitax/iterator.go

@@ -28,21 +28,22 @@ func NewITaxon() *ITaxon {
 // Iterator creates a new ITaxon iterator for the TaxonSet.
 // It starts a goroutine to send Taxon instances from the set to the iterator's source channel.
 func (set *TaxonSet) Iterator() *ITaxon {
-	i := NewITaxon()
+	return set.Sort().Iterator()
+	// i := NewITaxon()
 
-	go func() {
-		for _, t := range set.set {
-			taxon := &Taxon{
-				Taxonomy: set.taxonomy,
-				Metadata: nil,
-				Node:     t,
-			}
-			i.Push(taxon)
-		}
-		close(i.source)
-	}()
+	// go func() {
+	// 	for _, t := range set.set {
+	// 		taxon := &Taxon{
+	// 			Taxonomy: set.taxonomy,
+	// 			Metadata: nil,
+	// 			Node:     t,
+	// 		}
+	// 		i.Push(taxon)
+	// 	}
+	// 	close(i.source)
+	// }()
 
-	return i
+	// return i
 }
 
 // Iterator creates a new ITaxon iterator for the TaxonSlice.

pkg/obitax/taxonomy.go

@@ -386,7 +386,7 @@ func (taxonomy *Taxonomy) InsertPathString(path []string) (*Taxonomy, error) {
 		if err != nil {
 			return nil, err
 		}
-		root.SetName(scientific_name, "scientificName")
+		root.SetName(scientific_name, "scientific name")
 	}
 
 	var current *Taxon