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Fisrt functional version

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This commit is contained in:
Eric Coissac
2024-11-14 19:10:23 +01:00
parent 9471fedfa1
commit 03f4e88a17
26 changed files with 908 additions and 307 deletions
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8
pkg/obiformats/csv_writer.go
View File

@ -30,14 +30,10 @@ func CSVRecord(sequence *obiseq.BioSequence, opt Options) []string {
if opt.CSVTaxon() {
taxid := sequence.Taxid()
sn, ok := sequence.GetAttribute("scientific_name")
sn, ok := sequence.GetStringAttribute("scientific_name")
if !ok {
if taxid == 1 {
sn = "root"
} else {
sn = opt.CSVNAValue()
}
sn = opt.CSVNAValue()
}
record = append(record, fmt.Sprint(taxid), fmt.Sprint(sn))

47
pkg/obiformats/ncbitaxdump/read.go
View File

@ -7,7 +7,6 @@ import (
"io"
"os"
"path"
"strconv"
"strings"
log "github.com/sirupsen/logrus"
@ -26,24 +25,16 @@ func loadNodeTable(reader io.Reader, taxonomy *obitax.Taxonomy) {
for record, err := file.Read(); err == nil; record, err = file.Read() {
n++
taxid, err := strconv.Atoi(strings.TrimSpace(record[0]))
if err != nil {
log.Panicf("Cannot read taxon taxid at line %d: %v", n, err)
}
parent, err := strconv.Atoi(strings.TrimSpace(record[1]))
if err != nil {
log.Panicf("Cannot read taxon parent taxid at line %d: %v", n, err)
}
taxid := strings.TrimSpace(record[0])
parent := strings.TrimSpace(record[1])
rank := strings.TrimSpace(record[2])
taxonomy.AddNewTaxa(taxid, parent, rank, true, true)
}
_, err := taxonomy.AddTaxon(taxid, parent, rank, taxid == "1", false)
taxonomy.ReindexParent()
if err != nil {
log.Fatalf("Error adding taxon %s: %v\n", taxid, err)
}
}
}
func loadNameTable(reader io.Reader, taxonomy *obitax.Taxonomy, onlysn bool) int {
@ -65,18 +56,14 @@ func loadNameTable(reader io.Reader, taxonomy *obitax.Taxonomy, onlysn bool) int
}
record := strings.Split(string(line), "|")
taxid, err := strconv.Atoi(strings.TrimSpace(record[0]))
if err != nil {
log.Panicf("Cannot read taxon name taxid at line %d: %v", l, err)
}
taxid := strings.TrimSpace(record[0])
name := strings.TrimSpace(record[1])
classname := strings.TrimSpace(record[3])
if !onlysn || classname == "scientific name" {
n++
taxonomy.AddNewName(taxid, &name, &classname)
taxonomy.Taxon(taxid).SetName(name, classname)
}
}
@ -94,18 +81,10 @@ func loadMergedTable(reader io.Reader, taxonomy *obitax.Taxonomy) int {
for record, err := file.Read(); err == nil; record, err = file.Read() {
n++
oldtaxid, err := strconv.Atoi(strings.TrimSpace(record[0]))
oldtaxid := strings.TrimSpace(record[0])
newtaxid := strings.TrimSpace(record[1])
if err != nil {
log.Panicf("Cannot read alias taxid at line %d: %v", n, err)
}
newtaxid, err := strconv.Atoi(strings.TrimSpace(record[1]))
if err != nil {
log.Panicf("Cannot read alias new taxid at line %d: %v", n, err)
}
taxonomy.AddNewAlias(newtaxid, oldtaxid)
taxonomy.AddAlias(newtaxid, oldtaxid, false)
}
return n
@ -113,7 +92,7 @@ func loadMergedTable(reader io.Reader, taxonomy *obitax.Taxonomy) int {
func LoadNCBITaxDump(directory string, onlysn bool) (*obitax.Taxonomy, error) {
taxonomy := obitax.NewTaxonomy()
taxonomy := obitax.NewTaxonomy("NCBI Taxonomy", "taxon", "[[:digit:]]")
//
// Load the Taxonomy nodes