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Add the --taxonomic-path option to obiannotate

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Former-commit-id: 385309a1c4bc5ed33aeaafc63eedb9fc552f78a6
This commit is contained in:
Eric Coissac
2024-02-27 20:10:26 +01:00
parent 4127ddb26f
commit 4a0b20484f
5 changed files with 72 additions and 0 deletions
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20
pkg/obitax/sequence_methods.go
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@ -2,6 +2,7 @@ package obitax
import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
log "github.com/sirupsen/logrus"
)
// Setting the taxon at a given rank for a given sequence.
@ -46,3 +47,22 @@ func (taxonomy *Taxonomy) SetGenus(sequence *obiseq.BioSequence) *TaxNode {
func (taxonomy *Taxonomy) SetFamily(sequence *obiseq.BioSequence) *TaxNode {
return taxonomy.SetTaxonAtRank(sequence, "family")
}
func (taxonomy *Taxonomy) SetPath(sequence *obiseq.BioSequence) string {
taxid, err := taxonomy.Taxon(sequence.Taxid())
if err != nil {
log.Fatalf("Taxid %d not defined in the current taxonomy", sequence.Taxid())
}
path, err := taxid.Path()
if err != nil {
log.Fatalf("Taxonomy index error: %v", err)
}
tpath := path.String()
sequence.SetAttribute("taxonomic_path", tpath)
return tpath
}