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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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22
pkg/obiseq/biosequenceslice.go
View File

@ -1,6 +1,9 @@
package obiseq
import (
"errors"
"fmt"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obilog"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
@ -182,11 +185,26 @@ func (s *BioSequenceSlice) SortOnLength(reverse bool) {
})
}
func (s *BioSequenceSlice) ExtractTaxonomy(taxonomy *obitax.Taxonomy) (*obitax.Taxonomy, error) {
func (s *BioSequenceSlice) ExtractTaxonomy(taxonomy *obitax.Taxonomy, seqAsTaxa bool) (*obitax.Taxonomy, error) {
var err error
for _, s := range *s {
taxonomy, err = taxonomy.InsertPathString(s.Path())
path := s.Path()
if seqAsTaxa {
if len(path) == 0 {
return nil, fmt.Errorf("sequence %v has no path", s.Id())
}
last := path[len(path)-1]
taxname, _ := obiutils.SplitInTwo(last, ':')
if idx, ok := s.GetIntAttribute("seq_number"); !ok {
return nil, errors.New("sequences are not numbered")
} else {
path = append(path, fmt.Sprintf("%s:SEQ%010d [%s]@sequence", taxname, idx, s.Id()))
}
}
taxonomy, err = taxonomy.InsertPathString(path)
if err != nil {
return nil, err