skbio.tree.TreeNode.to_taxonomy#
- TreeNode.to_taxonomy(allow_empty=False, filter_f=None)[source]#
Return a taxonomy representation of self.
- Parameters:
- allow_emptybool, optional
Allow gaps the taxonomy (e.g., internal nodes without names).
- filter_ffunction, optional
Specify a filtering function that returns True if the lineage is to be returned. This function must accept a
TreeNode
as its first parameter, and alist
that represents the lineage as the second parameter.
- Yields:
- tuple
(tip, [lineage])
wheretip
corresponds to a tip in the tree and[lineage]
is the expanded names from root to tip.None
and empty strings are omitted from the lineage.
Notes
If
allow_empty
is True and the root node does not have a name, that name will not be included. This is because it is common to have multiple domains represented in the taxonomy, which would result in a root node that does not have a name and does not make sense to represent in the output.Examples
>>> from skbio.tree import TreeNode >>> lineages = {'1': ['Bacteria', 'Firmicutes', 'Clostridia'], ... '2': ['Bacteria', 'Firmicutes', 'Bacilli'], ... '3': ['Bacteria', 'Bacteroidetes', 'Sphingobacteria'], ... '4': ['Archaea', 'Euryarchaeota', 'Thermoplasmata'], ... '5': ['Archaea', 'Euryarchaeota', 'Thermoplasmata'], ... '6': ['Archaea', 'Euryarchaeota', 'Halobacteria'], ... '7': ['Archaea', 'Euryarchaeota', 'Halobacteria'], ... '8': ['Bacteria', 'Bacteroidetes', 'Sphingobacteria'], ... '9': ['Bacteria', 'Bacteroidetes', 'Cytophagia']} >>> tree = TreeNode.from_taxonomy(lineages.items()) >>> lineages = sorted([(n.name, l) for n, l in tree.to_taxonomy()]) >>> for name, lineage in lineages: ... print(name, '; '.join(lineage)) 1 Bacteria; Firmicutes; Clostridia 2 Bacteria; Firmicutes; Bacilli 3 Bacteria; Bacteroidetes; Sphingobacteria 4 Archaea; Euryarchaeota; Thermoplasmata 5 Archaea; Euryarchaeota; Thermoplasmata 6 Archaea; Euryarchaeota; Halobacteria 7 Archaea; Euryarchaeota; Halobacteria 8 Bacteria; Bacteroidetes; Sphingobacteria 9 Bacteria; Bacteroidetes; Cytophagia