mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
107 lines
3.0 KiB
Go
107 lines
3.0 KiB
Go
package obiseq
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import (
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
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)
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func (s *BioSequence) Taxon(taxonomy *obitax.Taxonomy) *obitax.Taxon {
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taxid := s.Taxid()
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if taxid == "NA" {
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return nil
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}
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return taxonomy.Taxon(taxid)
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}
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// Taxid returns the taxonomic ID associated with the BioSequence.
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//
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// It retrieves the "taxid" attribute from the BioSequence's attributes map.
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// If the attribute is not found, the function returns 1 as the default taxonomic ID.
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// The taxid 1 corresponds to the root taxonomic level.
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//
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// The function returns an integer representing the taxonomic ID.
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func (s *BioSequence) Taxid() (taxid string) {
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var ok bool
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if s.taxon != nil {
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taxid = s.taxon.String()
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ok = true
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} else {
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taxid, ok = s.GetStringAttribute("taxid")
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}
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if !ok {
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taxid = "NA"
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}
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return taxid
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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 (sequence *BioSequence) SetTaxonAtRank(taxonomy *obitax.Taxonomy, rank string) *obitax.Taxon {
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var taxonAtRank *obitax.Taxon
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taxon := sequence.Taxon(taxonomy)
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taxonAtRank = nil
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if taxon != 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.String())
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sequence.SetAttribute(rank+"_name", taxonAtRank.ScientificName())
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} else {
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sequence.SetAttribute(rank+"_taxid", "NA")
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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 (sequence *BioSequence) SetSpecies(taxonomy *obitax.Taxonomy) *obitax.Taxon {
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return sequence.SetTaxonAtRank(taxonomy, "species")
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}
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// Setting the genus of a sequence.
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func (sequence *BioSequence) SetGenus(taxonomy *obitax.Taxonomy) *obitax.Taxon {
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return sequence.SetTaxonAtRank(taxonomy, "genus")
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}
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// Setting the family of a sequence.
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func (sequence *BioSequence) SetFamily(taxonomy *obitax.Taxonomy) *obitax.Taxon {
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return sequence.SetTaxonAtRank(taxonomy, "family")
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}
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func (sequence *BioSequence) SetPath(taxonomy *obitax.Taxonomy) string {
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taxon := sequence.Taxon(taxonomy)
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path := taxon.Path()
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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 (sequence *BioSequence) SetScientificName(taxonomy *obitax.Taxonomy) string {
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taxon := sequence.Taxon(taxonomy)
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name := taxon.ScientificName()
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sequence.SetAttribute("scienctific_name", name)
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return name
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}
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func (sequence *BioSequence) SetTaxonomicRank(taxonomy *obitax.Taxonomy) string {
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taxon := sequence.Taxon(taxonomy)
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rank := taxon.Rank()
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sequence.SetAttribute("taxonomic_rank", rank)
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return rank
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}
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