mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
93 lines
2.7 KiB
Go
93 lines
2.7 KiB
Go
package obitax
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import (
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiseq"
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log "github.com/sirupsen/logrus"
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)
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// Setting the taxon at a given rank for a given sequence.
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//
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// Two attributes are added to the sequence. One named by the rank name stores
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// the taxid, a second named by the rank name suffixed with '_name' contains the
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// Scientific name of the genus.
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// If the taxon at the given rank doesn't exist for the taxonomy annotation
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// of the sequence, nothing happens.
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func (taxonomy *Taxonomy) SetTaxonAtRank(sequence *obiseq.BioSequence, rank string) *TaxNode {
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var taxonAtRank *TaxNode
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taxid := sequence.Taxid()
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taxon, err := taxonomy.Taxon(taxid)
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taxonAtRank = nil
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if err == nil {
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taxonAtRank = taxon.TaxonAtRank(rank)
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if taxonAtRank != nil {
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// log.Printf("Taxid: %d Rank: %s --> proposed : %d (%s)", taxid, rank, taxonAtRank.taxid, *(taxonAtRank.scientificname))
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sequence.SetAttribute(rank+"_taxid", taxonAtRank.taxid)
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sequence.SetAttribute(rank+"_name", *taxonAtRank.scientificname)
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} else {
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sequence.SetAttribute(rank+"_taxid", -1)
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sequence.SetAttribute(rank+"_name", "NA")
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}
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}
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return taxonAtRank
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}
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// Setting the species of a sequence.
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func (taxonomy *Taxonomy) SetSpecies(sequence *obiseq.BioSequence) *TaxNode {
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return taxonomy.SetTaxonAtRank(sequence, "species")
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}
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// Setting the genus of a sequence.
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func (taxonomy *Taxonomy) SetGenus(sequence *obiseq.BioSequence) *TaxNode {
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return taxonomy.SetTaxonAtRank(sequence, "genus")
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}
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// Setting the family of a sequence.
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func (taxonomy *Taxonomy) SetFamily(sequence *obiseq.BioSequence) *TaxNode {
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return taxonomy.SetTaxonAtRank(sequence, "family")
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}
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func (taxonomy *Taxonomy) SetPath(sequence *obiseq.BioSequence) string {
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taxid, err := taxonomy.Taxon(sequence.Taxid())
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if err != nil {
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log.Fatalf("Taxid %d not defined in the current taxonomy", sequence.Taxid())
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}
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path, err := taxid.Path()
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if err != nil {
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log.Fatalf("Taxonomy index error: %v", err)
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}
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tpath := path.String()
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sequence.SetAttribute("taxonomic_path", tpath)
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return tpath
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}
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func (taxonomy *Taxonomy) SetScientificName(sequence *obiseq.BioSequence) string {
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taxid, err := taxonomy.Taxon(sequence.Taxid())
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if err != nil {
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log.Fatalf("Taxid %d not defined in the current taxonomy", sequence.Taxid())
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}
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sequence.SetAttribute("scienctific_name", taxid.ScientificName())
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return taxid.ScientificName()
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}
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func (taxonomy *Taxonomy) SetTaxonomicRank(sequence *obiseq.BioSequence) string {
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taxid, err := taxonomy.Taxon(sequence.Taxid())
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if err != nil {
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log.Fatalf("Taxid %d not defined in the current taxonomy", sequence.Taxid())
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}
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sequence.SetAttribute("taxonomic_rank", taxid.Rank())
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return taxid.Rank()
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}
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