mirror of
https://github.com/metabarcoding/obitools4.git
synced 2025-06-29 16:20:46 +00:00
98 lines
2.3 KiB
Go
98 lines
2.3 KiB
Go
package obiseq
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import (
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log "github.com/sirupsen/logrus"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
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"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
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)
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func IsAValidTaxon(taxonomy *obitax.Taxonomy, withAutoCorrection ...bool) SequencePredicate {
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// deprecatedTaxidsWarning := make(map[string]bool)
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autocorrection := false
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if len(withAutoCorrection) > 0 {
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autocorrection = withAutoCorrection[0]
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}
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f := func(sequence *BioSequence) bool {
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taxon := sequence.Taxon(taxonomy)
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if taxon != nil {
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taxid := sequence.Taxid()
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ttaxid := taxon.String()
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if taxid != ttaxid {
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if autocorrection {
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sequence.SetTaxid(ttaxid)
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log.Printf(
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"Sequence %s : Taxid %s updated with %s",
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sequence.Id(),
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taxid,
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ttaxid,
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)
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} // else {
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// if _, ok := deprecatedTaxidsWarning[taxid]; !ok {
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// deprecatedTaxidsWarning[taxid] = true
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// log.Printf("Taxid %d is deprecated and must be replaced by %d", taxid, taxon.taxid)
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// }
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// }
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}
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}
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return taxon != nil
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}
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return f
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}
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// A function that takes a taxonomy and a taxid as arguments and returns a function that takes a
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// pointer to a BioSequence as an argument and returns a boolean.
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func IsSubCladeOf(taxonomy *obitax.Taxonomy, parent *obitax.Taxon) SequencePredicate {
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f := func(sequence *BioSequence) bool {
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taxon := sequence.Taxon(taxonomy)
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return taxon != nil && taxon.IsSubCladeOf(parent)
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}
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return f
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}
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func IsSubCladeOfSlot(taxonomy *obitax.Taxonomy, key string) SequencePredicate {
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f := func(sequence *BioSequence) bool {
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val, ok := sequence.GetStringAttribute(key)
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if ok {
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parent, _, err := taxonomy.Taxon(val)
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if err != nil {
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obilog.Warnf("%s: %s is unkown from the taxonomy (%v)", sequence.Id(), val, err)
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}
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taxon := sequence.Taxon(taxonomy)
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return parent != nil && taxon != nil && taxon.IsSubCladeOf(parent)
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}
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return false
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}
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return f
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}
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func HasRequiredRank(taxonomy *obitax.Taxonomy, rank string) SequencePredicate {
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if !obiutils.Contains(taxonomy.RankList(), rank) {
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log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
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rank,
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taxonomy.RankList())
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}
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f := func(sequence *BioSequence) bool {
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taxon := sequence.Taxon(taxonomy)
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return taxon != nil && taxon.HasRankDefined(rank)
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}
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return f
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}
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