obitools/obitools4
2
0
Fork 0
mirror of https://github.com/metabarcoding/obitools4.git synced 2025-06-29 16:20:46 +00:00
Code Issues Packages Projects Releases Wiki Activity

Add managment of the taxonomy alias politic

Browse Source
This commit is contained in:
Eric Coissac
2025-02-10 14:05:47 +01:00
parent e2563cd8df
commit 6a8061cc4f
16 changed files with 114 additions and 48 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
pkg/obitax/iterator.go
View File

@ -216,7 +216,7 @@ func (taxon *Taxon) ISubTaxonomy() *ITaxon {
}
func (taxonomy *Taxonomy) ISubTaxonomy(taxid string) *ITaxon {
taxon, err := taxonomy.Taxon(taxid)
taxon, _, err := taxonomy.Taxon(taxid)
if err != nil {
return nil

4
pkg/obitax/ncbitaxdump_read.go
View File

@ -91,7 +91,7 @@ func loadNameTable(reader io.Reader, taxonomy *Taxonomy, onlysn bool) int {
if !onlysn || classname == "scientific name" {
n++
taxon, err := taxonomy.Taxon(taxid)
taxon, _, err := taxonomy.Taxon(taxid)
if err != nil {
log.Fatalf("%s: is unknown from the taxonomy", taxid)
@ -202,7 +202,7 @@ func LoadNCBITaxDump(directory string, onlysn bool) (*Taxonomy, error) {
n = loadMergedTable(buffered, taxonomy)
log.Printf("%d merged taxa read\n", n)
root, err := taxonomy.Taxon("1")
root, _, err := taxonomy.Taxon("1")
if err != nil {
log.Fatal("cannot find the root taxon (1) in the NCBI tax dump")

2
pkg/obitax/ncbitaxdump_readtar.go
View File

@ -134,7 +134,7 @@ func LoadNCBITarTaxDump(path string, onlysn bool) (*Taxonomy, error) {
n = loadMergedTable(buffered, taxonomy)
log.Printf("%d merged taxa read\n", n)
root, err := taxonomy.Taxon("1")
root, _, err := taxonomy.Taxon("1")
if err != nil {
log.Fatal("cannot find the root taxon (1) in the NCBI tax dump")

14
pkg/obitax/taxonomy.go
View File

@ -129,28 +129,30 @@ func (taxonomy *Taxonomy) TaxidString(id string) (string, error) {
// Returns:
// - A pointer to the Taxon instance associated with the provided taxid.
// - If the taxid is unknown, the method will log a fatal error.
func (taxonomy *Taxonomy) Taxon(taxid string) (*Taxon, error) {
func (taxonomy *Taxonomy) Taxon(taxid string) (*Taxon, bool, error) {
taxonomy = taxonomy.OrDefault(false)
if taxonomy == nil {
return nil, errors.New("cannot extract taxon from nil taxonomy")
return nil, false, errors.New("cannot extract taxon from nil taxonomy")
}
id, err := taxonomy.Id(taxid)
if err != nil {
return nil, fmt.Errorf("Taxid %s: %v", taxid, err)
return nil, false, fmt.Errorf("Taxid %s: %v", taxid, err)
}
taxon := taxonomy.nodes.Get(id)
isAlias := taxon.Node.id != id
if taxon == nil {
return nil,
false,
fmt.Errorf("Taxid %s is not part of the taxonomy %s",
taxid,
taxonomy.name)
}
return taxon, nil
return taxon, isAlias, nil
}
// AsTaxonSet returns the set of taxon nodes contained within the Taxonomy.
@ -385,7 +387,7 @@ func (taxonomy *Taxonomy) InsertPathString(path []string) (*Taxonomy, error) {
}
var current *Taxon
current, err = taxonomy.Taxon(taxid)
current, _, err = taxonomy.Taxon(taxid)
if err != nil {
return nil, err
@ -396,7 +398,7 @@ func (taxonomy *Taxonomy) InsertPathString(path []string) (*Taxonomy, error) {
}
for _, id := range path[1:] {
taxon, err := taxonomy.Taxon(id)
taxon, _, err := taxonomy.Taxon(id)
if err == nil {
if !current.SameAs(taxon.Parent()) {
return nil, errors.New("path is not consistent with the taxonomy, parent mismatch")