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Add managment of the taxonomy alias politic

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This commit is contained in:
Eric Coissac
2025-02-10 14:05:47 +01:00
parent e2563cd8df
commit 6a8061cc4f
16 changed files with 114 additions and 48 deletions
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8
pkg/obiseq/taxonomy_lca.go
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@@ -4,6 +4,7 @@ import (
"math"
"strings"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
log "github.com/sirupsen/logrus"
)
@@ -15,7 +16,7 @@ func (sequence *BioSequence) TaxonomicDistribution(taxonomy *obitax.Taxonomy) ma
taxonomy = taxonomy.OrDefault(true)
for taxid, v := range taxids {
t, err := taxonomy.Taxon(taxid)
t, isAlias, err := taxonomy.Taxon(taxid)
if err != nil {
log.Fatalf(
"On sequence %s taxid %s is not defined in taxonomy: %s (%v)",
@@ -25,6 +26,11 @@ func (sequence *BioSequence) TaxonomicDistribution(taxonomy *obitax.Taxonomy) ma
err,
)
}
if isAlias && obidefault.FailOnTaxonomy() {
log.Fatalf("On sequence %s taxid %s is an alias on %s",
sequence.Id(), taxid, t.String())
}
taxons[t.Node] = v
}
return taxons