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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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24
pkg/obiformats/newick_write.go
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@ -54,7 +54,7 @@ func (tree *Tree) Newick(level int, taxid, scientific_name, rank bool) string {
if scientific_name {
buffer.WriteByte(' ')
}
buffer.WriteByte('-')
// buffer.WriteByte('-')
if taxid {
buffer.WriteString(*tree.TaxNode.Id())
if rank {
@ -64,7 +64,7 @@ func (tree *Tree) Newick(level int, taxid, scientific_name, rank bool) string {
if rank {
buffer.WriteString(tree.TaxNode.Rank())
}
buffer.WriteByte('-')
//buffer.WriteByte('-')
}
if scientific_name || taxid || rank {
buffer.WriteByte('\'')
@ -85,24 +85,14 @@ func Newick(taxa *obitax.TaxonSet, taxid, scientific_name, rank bool) string {
return ""
}
iterator := taxa.Sort().Iterator()
root := taxa.Sort().Get(0)
tree, err := taxa.AsPhyloTree(root)
nodes := make(map[*string]*Tree, taxa.Len())
trees := make([]*Tree, 0)
for iterator.Next() {
taxon := iterator.Get()
tree := &Tree{TaxNode: taxon.Node}
if parent, ok := nodes[taxon.Parent().Node.Id()]; ok {
parent.Children = append(parent.Children, tree)
} else {
trees = append(trees, tree)
}
nodes[taxon.Node.Id()] = tree
if err != nil {
log.Fatalf("Cannot build taxonomy tree: %v", err)
}
return trees[0].Newick(0, taxid, scientific_name, rank)
return tree.Newick(0)
}
func WriteNewick(iterator *obitax.ITaxon,