obitools/obitools4
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Changes to be committed:

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modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitaxonomy/main.go
	modified:   pkg/obiformats/csvtaxdump_read.go
	modified:   pkg/obiformats/ecopcr_read.go
	modified:   pkg/obiformats/ncbitaxdump_read.go
	modified:   pkg/obiformats/ncbitaxdump_readtar.go
	modified:   pkg/obiformats/newick_write.go
	modified:   pkg/obiformats/options.go
	modified:   pkg/obiformats/taxonomy_read.go
	modified:   pkg/obiformats/universal_read.go
	modified:   pkg/obiiter/extract_taxonomy.go
	modified:   pkg/obioptions/options.go
	modified:   pkg/obioptions/version.go
	new file:   pkg/obiphylo/tree.go
	modified:   pkg/obiseq/biosequenceslice.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitools/obiconvert/sequence_reader.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitaxonomy/obitaxonomy.go
	modified:   pkg/obitools/obitaxonomy/options.go
	deleted:    sample/.DS_Store
This commit is contained in:
Eric Coissac
2025-06-04 09:48:10 +02:00
parent 3424d3057f
commit 6cb7a5a352
23 changed files with 230 additions and 56 deletions
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3
cmd/obitools/obitag/main.go
View File

@ -11,6 +11,7 @@ import (
"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/obitag"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitools/obitaxonomy"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
@ -58,7 +59,7 @@ func main() {
}
if taxo == nil {
taxo, err = references.ExtractTaxonomy(nil)
taxo, err = references.ExtractTaxonomy(nil, obitaxonomy.CLINewickWithLeaves())
if err != nil {
log.Fatalf("No taxonomy specified or extractable from reference database: %v", err)

3
cmd/obitools/obitaxonomy/main.go
View File

@ -62,12 +62,13 @@ func main() {
case obitaxonomy.CLIExtractTaxonomy():
iter, err := obiconvert.CLIReadBioSequences(args...)
iter = iter.NumberSequences(1, true)
if err != nil {
log.Fatalf("Cannot extract taxonomy: %v", err)
}
taxonomy, err := iter.ExtractTaxonomy()
taxonomy, err := iter.ExtractTaxonomy(obitaxonomy.CLINewickWithLeaves())
if err != nil {
log.Fatalf("Cannot extract taxonomy: %v", err)