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Adds possibility to extract a taxonomy from taxonomic path included in sequence files

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This commit is contained in:
Eric Coissac
2025-01-30 11:18:21 +01:00
parent 2452aef7a9
commit 0df082da06
20 changed files with 460 additions and 173 deletions
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28
cmd/obitools/obitaxonomy/main.go
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@ -5,6 +5,7 @@ import (
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obiconvert"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitaxonomy"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@ -19,7 +20,6 @@ func main() {
var iterator *obitax.ITaxon
switch {
case obitaxonomy.CLIDownloadNCBI():
err := obitaxonomy.CLIDownloadNCBITaxdump()
if err != nil {
@ -29,16 +29,34 @@ func main() {
os.Exit(0)
case obitaxonomy.CLIExtractTaxonomy():
iter, err := obiconvert.CLIReadBioSequences(args...)
if err != nil {
log.Fatalf("Cannot extract taxonomy: %v", err)
}
taxonomy, err := iter.ExtractTaxonomy()
if err != nil {
log.Fatalf("Cannot extract taxonomy: %v", err)
}
taxonomy.SetAsDefault()
log.Infof("Number of extracted taxa: %d", taxonomy.Len())
iterator = taxonomy.AsTaxonSet().Sort().Iterator()
case obitaxonomy.CLIDumpSubtaxonomy():
iterator = obitaxonomy.CLISubTaxonomyIterator()
case obitaxonomy.CLIRequestsPathForTaxid() != "NA":
taxon := obitax.DefaultTaxonomy().Taxon(obitaxonomy.CLIRequestsPathForTaxid())
taxon, err := obitax.DefaultTaxonomy().Taxon(obitaxonomy.CLIRequestsPathForTaxid())
if taxon == nil {
log.Fatalf("Cannot identify the requested taxon: %s",
obitaxonomy.CLIRequestsPathForTaxid())
if err != nil {
log.Fatalf("Cannot identify the requested taxon: %s (%v)",
obitaxonomy.CLIRequestsPathForTaxid(), err)
}
s := taxon.Path()