mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
142 lines
3.1 KiB
Go
142 lines
3.1 KiB
Go
package ncbitaxdump
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import (
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"bufio"
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"encoding/csv"
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"fmt"
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"io"
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"os"
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"path"
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"strconv"
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"strings"
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
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)
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func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
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file := csv.NewReader(reader)
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file.Comma = '|'
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file.Comment = '#'
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file.TrimLeadingSpace = true
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file.ReuseRecord = true
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for record, err := file.Read(); err == nil; record, err = file.Read() {
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taxid, _ := strconv.Atoi(strings.TrimSpace(record[0]))
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parent, _ := strconv.Atoi(strings.TrimSpace(record[1]))
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rank := strings.TrimSpace(record[2])
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taxonomy.AddNewTaxa(taxid, parent, rank, true, true)
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}
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taxonomy.ReindexParent()
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}
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func loadNameTable(reader io.Reader, taxonomy *obitax.Taxonomy, onlysn bool) int {
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// file := csv.NewReader(reader)
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// file.Comma = '|'
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// file.Comment = '#'
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// file.TrimLeadingSpace = true
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// file.ReuseRecord = true
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// file.LazyQuotes = true
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file := bufio.NewReader(reader)
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n := 0
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for line, prefix, err := file.ReadLine(); err == nil; line, prefix, err = file.ReadLine() {
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if prefix {
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return -1
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}
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record := strings.Split(string(line), "|")
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taxid, _ := strconv.Atoi(strings.TrimSpace(record[0]))
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name := strings.TrimSpace(record[1])
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classname := strings.TrimSpace(record[3])
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if !onlysn || classname == "scientific name" {
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n++
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taxonomy.AddNewName(taxid, &name, &classname)
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}
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}
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return n
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}
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func loadMergedTable(reader io.Reader, taxonomy *obitax.Taxonomy) int {
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file := csv.NewReader(reader)
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file.Comma = '|'
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file.Comment = '#'
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file.TrimLeadingSpace = true
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file.ReuseRecord = true
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n := 0
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for record, err := file.Read(); err == nil; record, err = file.Read() {
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oldtaxid, _ := strconv.Atoi(strings.TrimSpace(record[0]))
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newtaxid, _ := strconv.Atoi(strings.TrimSpace(record[1]))
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n++
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taxonomy.AddNewAlias(newtaxid, oldtaxid)
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}
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return n
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}
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func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
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taxonomy := obitax.NewTaxonomy()
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//
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// Load the Taxonomy nodes
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//
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log.Printf("Loading Taxonomy nodes\n")
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nodefile, err := os.Open(path.Join(directory, "nodes.dmp"))
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if err != nil {
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return nil, fmt.Errorf("cannot open nodes file from '%s'",
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directory)
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}
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defer nodefile.Close()
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buffered := bufio.NewReader(nodefile)
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loadNodeTable(buffered, taxonomy)
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log.Printf("%d Taxonomy nodes read\n", taxonomy.Len())
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//
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// Load the Taxonomy nodes
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//
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log.Printf("Loading Taxon names\n")
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namefile, nerr := os.Open(path.Join(directory, "names.dmp"))
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if nerr != nil {
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return nil, fmt.Errorf("cannot open names file from '%s'",
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directory)
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}
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defer namefile.Close()
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n := loadNameTable(namefile, taxonomy, onlysn)
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log.Printf("%d taxon names read\n", n)
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//
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// Load the merged taxa
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//
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log.Printf("Loading Merged taxa\n")
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aliasfile, aerr := os.Open(path.Join(directory, "merged.dmp"))
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if aerr != nil {
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return nil, fmt.Errorf("cannot open merged file from '%s'",
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directory)
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}
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defer aliasfile.Close()
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buffered = bufio.NewReader(aliasfile)
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n = loadMergedTable(buffered, taxonomy)
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log.Printf("%d merged taxa read\n", n)
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return taxonomy, nil
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}
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