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https://github.com/metabarcoding/obitools4.git
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38 lines
1.2 KiB
Go
38 lines
1.2 KiB
Go
package obitax
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import (
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"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
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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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taxid := sequence.Taxid()
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taxon, err := taxonomy.Taxon(taxid)
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taxonAtRank := taxon.TaxonAtRank(rank)
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if err == nil && taxonAtRank != nil {
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sequence.SetAttribute(rank, taxonAtRank.taxid)
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sequence.SetAttribute(rank+"_name", taxonAtRank.scientificname)
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}
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return taxonAtRank
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}
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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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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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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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