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Adds the --silent-warning options to the obitools commands and removes the --pared-with option from some of the obitols commands.

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Eric Coissac
2025-03-25 16:44:46 +01:00
parent 2ab6f67d58
commit 5a3705b6bb
52 changed files with 151 additions and 90 deletions
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7
pkg/obiseq/taxonomy_methods.go
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@ -6,6 +6,7 @@ import (
log "github.com/sirupsen/logrus"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obidefault"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
)
@ -41,7 +42,7 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
taxon, isAlias, err = taxonomy.Taxon(taxid)
if err != nil {
logger := log.Warnf
logger := obilog.Warnf
if obidefault.FailOnTaxonomy() {
logger = log.Fatalf
}
@ -51,7 +52,7 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
if isAlias {
if obidefault.UpdateTaxid() {
log.Warnf("%s: Taxid: %v is updated to %s",
obilog.Warnf("%s: Taxid: %v is updated to %s",
s.Id(), taxid, taxon.String())
taxid = taxon.String()
} else {
@ -59,7 +60,7 @@ func (s *BioSequence) SetTaxid(taxid string, rank ...string) {
log.Fatalf("%s: Taxid: %v is an alias from taxonomy (%v) to %s",
s.Id(), taxid, taxonomy.Name(), taxon.String())
}
log.Warnf("%s: Taxid %v has to be updated to %s",
obilog.Warnf("%s: Taxid %v has to be updated to %s",
s.Id(), taxid, taxon.String())
}