Adds possibility to extract a taxonomy from taxonomic path included in sequence files

pkg/obitax/string_parser.go

@@ -0,0 +1,64 @@
+package obitax
+
+import (
+	"errors"
+	"strings"
+)
+
+// ParseTaxonString parses a string in the format "code:taxid [scientific name]@rank"
+// and returns the individual components. It handles extra whitespace around components.
+//
+// Parameters:
+//   - taxonStr: The string to parse in the format "code:taxid [scientific name]@rank"
+//
+// Returns:
+//   - code: The taxonomy code
+//   - taxid: The taxon identifier
+//   - scientificName: The scientific name (without brackets)
+//   - rank: The rank
+//   - error: An error if the string format is invalid
+func ParseTaxonString(taxonStr string) (code, taxid, scientificName, rank string, err error) {
+	// Trim any leading/trailing whitespace from the entire string
+	taxonStr = strings.TrimSpace(taxonStr)
+
+	// Split by '@' to separate rank
+	parts := strings.Split(taxonStr, "@")
+	if len(parts) > 2 {
+		return "", "", "", "", errors.New("invalid format: multiple '@' characters found")
+	}
+
+	mainPart := strings.TrimSpace(parts[0])
+	if len(parts) == 2 {
+		rank = strings.TrimSpace(parts[1])
+	} else {
+		rank = "no rank"
+	}
+
+	// Find scientific name part (enclosed in square brackets)
+	startBracket := strings.Index(mainPart, "[")
+	endBracket := strings.LastIndex(mainPart, "]")
+
+	if startBracket == -1 || endBracket == -1 || startBracket > endBracket {
+		return "", "", "", "", errors.New("invalid format: scientific name must be enclosed in square brackets")
+	}
+
+	// Extract and clean scientific name
+	scientificName = strings.TrimSpace(mainPart[startBracket+1 : endBracket])
+
+	// Process code:taxid part
+	idPart := strings.TrimSpace(mainPart[:startBracket])
+	idComponents := strings.Split(idPart, ":")
+
+	if len(idComponents) != 2 {
+		return "", "", "", "", errors.New("invalid format: missing taxonomy code separator ':'")
+	}
+
+	code = strings.TrimSpace(idComponents[0])
+	taxid = strings.TrimSpace(idComponents[1])
+
+	if code == "" || taxid == "" || scientificName == "" {
+		return "", "", "", "", errors.New("invalid format: code, taxid and scientific name cannot be empty")
+	}
+
+	return code, taxid, scientificName, rank, nil
+}