Make sequence files recognized as a taxonomy

pkg/obiformats/csviterator.go

@@ -0,0 +1,113 @@
+package obiformats
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiitercsv"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+)
+
+func CSVTaxaIterator(iterator *obitax.ITaxon, options ...WithOption) *obiitercsv.ICSVRecord {
+
+	opt := MakeOptions(options)
+	metakeys := make([]string, 0)
+
+	newIter := obiitercsv.NewICSVRecord()
+
+	newIter.Add(1)
+
+	batch_size := opt.BatchSize()
+
+	if opt.WithPattern() {
+		newIter.AppendField("query")
+		opt.pointer.with_metadata = append(opt.pointer.with_metadata, "query")
+	}
+
+	newIter.AppendField("taxid")
+	rawtaxid := opt.RawTaxid()
+
+	if opt.WithParent() {
+		newIter.AppendField("parent")
+	}
+
+	if opt.WithRank() {
+		newIter.AppendField("taxonomic_rank")
+	}
+
+	if opt.WithScientificName() {
+		newIter.AppendField("scientific_name")
+	}
+
+	if opt.WithMetadata() != nil {
+		metakeys = opt.WithMetadata()
+		for _, metadata := range metakeys {
+			newIter.AppendField(metadata)
+		}
+	}
+
+	if opt.WithPath() {
+		newIter.AppendField("path")
+	}
+
+	go func() {
+		newIter.WaitAndClose()
+	}()
+
+	go func() {
+		o := 0
+		data := make([]obiitercsv.CSVRecord, 0, batch_size)
+		for iterator.Next() {
+
+			taxon := iterator.Get()
+			record := make(obiitercsv.CSVRecord)
+
+			if opt.WithPattern() {
+				record["query"] = taxon.MetadataAsString("query")
+			}
+
+			if rawtaxid {
+				record["taxid"] = *taxon.Node.Id()
+			} else {
+				record["taxid"] = taxon.String()
+			}
+
+			if opt.WithParent() {
+				if rawtaxid {
+					record["parent"] = *taxon.Node.ParentId()
+				} else {
+					record["parent"] = taxon.Parent().String()
+				}
+			}
+
+			if opt.WithRank() {
+				record["taxonomic_rank"] = taxon.Rank()
+			}
+
+			if opt.WithScientificName() {
+				record["scientific_name"] = taxon.ScientificName()
+			}
+
+			if opt.WithPath() {
+				record["path"] = taxon.Path().String()
+			}
+
+			for _, key := range metakeys {
+				record[key] = taxon.MetadataAsString(key)
+			}
+
+			data = append(data, record)
+			if len(data) >= batch_size {
+				newIter.Push(obiitercsv.MakeCSVRecordBatch(opt.Source(), o, data))
+				data = make([]obiitercsv.CSVRecord, 0, batch_size)
+				o++
+			}
+
+		}
+
+		if len(data) > 0 {
+			newIter.Push(obiitercsv.MakeCSVRecordBatch(opt.Source(), o, data))
+		}
+
+		newIter.Done()
+	}()
+
+	return newIter
+}