Make sequence files recognized as a taxonomy

pkg/obiformats/csvtaxdump_read.go

@@ -0,0 +1,120 @@
+package obiformats
+
+import (
+	"encoding/csv"
+	"errors"
+	"strings"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+	log "github.com/sirupsen/logrus"
+)
+
+func LoadCSVTaxonomy(path string, onlysn bool) (*obitax.Taxonomy, error) {
+
+	log.Infof("Loading taxonomy from csv file: %s", path)
+
+	file, err := obiutils.Ropen(path)
+
+	if err != nil {
+		return nil, err
+	}
+
+	defer file.Close()
+
+	csvfile := csv.NewReader(file)
+
+	csvfile.Comma = ','
+	csvfile.ReuseRecord = false
+	csvfile.LazyQuotes = true
+	csvfile.Comment = '#'
+	csvfile.FieldsPerRecord = -1
+	csvfile.TrimLeadingSpace = true
+
+	header, err := csvfile.Read()
+
+	if err != nil {
+		log.Fatal(err)
+	}
+
+	taxidColIndex := -1
+	parentColIndex := -1
+	scientific_nameColIndex := -1
+	rankColIndex := -1
+
+	for i, colName := range header {
+		switch colName {
+		case "taxid":
+			taxidColIndex = i
+		case "parent":
+			parentColIndex = i
+		case "scientific_name":
+			scientific_nameColIndex = i
+		case "taxonomic_rank":
+			rankColIndex = i
+		}
+	}
+
+	if taxidColIndex == -1 {
+		return nil, errors.New("taxonomy file does not contain taxid column")
+	}
+
+	if parentColIndex == -1 {
+		return nil, errors.New("taxonomy file does not contain parent column")
+	}
+
+	if scientific_nameColIndex == -1 {
+		return nil, errors.New("taxonomy file does not contain scientific_name column")
+	}
+
+	if rankColIndex == -1 {
+		return nil, errors.New("taxonomy file does not contain rank column")
+	}
+
+	name := obiutils.RemoveAllExt(path)
+	short := obiutils.Basename(path)
+
+	line, err := csvfile.Read()
+	if err == nil {
+		parts := strings.Split(line[taxidColIndex], " ")
+		parts = strings.Split(parts[0], ":")
+		if len(parts) > 1 {
+			short = parts[0]
+		}
+	}
+
+	log.Infof("Taxonomy name: %s", name)
+	log.Infof("Taxon code: %s", short)
+
+	taxonomy := obitax.NewTaxonomy(name, short, obiutils.AsciiAlphaNumSet)
+
+	root := true
+	var taxon *obitax.Taxon
+
+	for err == nil {
+		taxid := line[taxidColIndex]
+		parent := line[parentColIndex]
+		scientific_name := line[scientific_nameColIndex]
+		rank := line[rankColIndex]
+
+		taxon, err = taxonomy.AddTaxon(taxid, parent, rank, root, false)
+
+		if err != nil {
+			log.Fatalf("cannot add taxon %s:  %v", taxid, err)
+		}
+
+		root = false
+
+		taxon.SetName(scientific_name, "scientific name")
+
+		line, err = csvfile.Read()
+	}
+
+	log.Infof("%d Taxa loaded", taxonomy.Len())
+
+	if !taxonomy.HasRoot() {
+		return nil, errors.New("taxonomy file does not contain root node")
+	}
+
+	return taxonomy, nil
+}