Make sequence files recognized as a taxonomy

pkg/obiformats/ncbitaxdump_readtar.go

@@ -0,0 +1,147 @@
+package obiformats
+
+import (
+	"archive/tar"
+	"bufio"
+	"fmt"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+
+	log "github.com/sirupsen/logrus"
+)
+
+func IsNCBITarTaxDump(path string) bool {
+
+	file, err := obiutils.Ropen(path)
+
+	if err != nil {
+		return false
+	}
+
+	defer file.Close()
+
+	citations := false
+	division := false
+	gencode := false
+	names := false
+	delnodes := false
+	gc := false
+	merged := false
+	nodes := false
+
+	tarfile := tar.NewReader(file)
+
+	header, err := tarfile.Next()
+
+	for err == nil {
+		name := header.Name
+
+		if header.Typeflag == tar.TypeReg {
+			switch name {
+			case "citations.dmp":
+				citations = true
+			case "division.dmp":
+				division = true
+			case "gencode.dmp":
+				gencode = true
+			case "names.dmp":
+				names = true
+			case "delnodes.dmp":
+				delnodes = true
+			case "gc.prt":
+				gc = true
+			case "merged.dmp":
+				merged = true
+			case "nodes.dmp":
+				nodes = true
+			}
+		}
+		header, err = tarfile.Next()
+	}
+
+	return citations && division && gencode && names && delnodes && gc && merged && nodes
+}
+
+func LoadNCBITarTaxDump(path string, onlysn bool) (*obitax.Taxonomy, error) {
+
+	taxonomy := obitax.NewTaxonomy("NCBI Taxonomy", "taxon", obiutils.AsciiDigitSet)
+
+	//
+	// Load the Taxonomy nodes
+	//
+
+	log.Printf("Loading Taxonomy nodes\n")
+
+	file, err := obiutils.Ropen(path)
+	if err != nil {
+		return nil, fmt.Errorf("cannot open taxonomy file from '%s'",
+			path)
+	}
+
+	nodefile, err := obiutils.TarFileReader(file, "nodes.dmp")
+	if err != nil {
+		file.Close()
+		return nil, fmt.Errorf("cannot open nodes file from '%s'",
+			path)
+	}
+
+	buffered := bufio.NewReader(nodefile)
+	loadNodeTable(buffered, taxonomy)
+	log.Printf("%d Taxonomy nodes read\n", taxonomy.Len())
+	file.Close()
+
+	//
+	// Load the Taxonomy nodes
+	//
+
+	log.Printf("Loading Taxon names\n")
+
+	file, err = obiutils.Ropen(path)
+	if err != nil {
+		return nil, fmt.Errorf("cannot open taxonomy file from '%s'",
+			path)
+	}
+
+	namefile, nerr := obiutils.TarFileReader(file, "names.dmp")
+	if nerr != nil {
+		file.Close()
+		return nil, fmt.Errorf("cannot open names file from '%s'",
+			path)
+	}
+	n := loadNameTable(namefile, taxonomy, onlysn)
+	log.Printf("%d taxon names read\n", n)
+	file.Close()
+
+	//
+	// Load the merged taxa
+	//
+
+	log.Printf("Loading Merged taxa\n")
+	file, err = obiutils.Ropen(path)
+	if err != nil {
+		return nil, fmt.Errorf("cannot open taxonomy file from '%s'",
+			path)
+	}
+
+	aliasfile, aerr := obiutils.TarFileReader(file, "merged.dmp")
+	if aerr != nil {
+		file.Close()
+		return nil, fmt.Errorf("cannot open merged file from '%s'",
+			path)
+	}
+
+	buffered = bufio.NewReader(aliasfile)
+	n = loadMergedTable(buffered, taxonomy)
+	log.Printf("%d merged taxa read\n", n)
+
+	root, _, err := taxonomy.Taxon("1")
+
+	if err != nil {
+		log.Fatal("cannot find the root taxon (1) in the NCBI tax dump")
+	}
+
+	taxonomy.SetRoot(root)
+
+	return taxonomy, nil
+}