skbio.tree.TreeNode.from_taxdump#

classmethod TreeNode.from_taxdump(nodes, names=None)[source]#

Construct a tree from the NCBI taxonomy database.

Parameters:

nodespd.DataFrame: Taxon hierarchy.
namespd.DataFrame or dict, optional: Taxon names.

Returns:

TreeNode: The constructed tree.

Raises:

ValueError: If there is no top-level node.
ValueError: If there are more than one top-level node.

See also

from_taxonomy
skbio.io.format.taxdump

Notes

nodes and names correspond to “nodes.dmp” and “names.dmp” of the NCBI taxonomy database. The should be read into data frames using skbio.io.read prior to this operation. Alternatively, names may be provided as a dictionary. If names is omitted, taxonomy IDs be used as taxon names.

Examples

>>> import pandas as pd
>>> from skbio.tree import TreeNode
>>> nodes = pd.DataFrame([
...             [1, 1, 'no rank'],
...             [2, 1, 'domain'],
...             [3, 1, 'domain'],
...             [4, 2, 'phylum'],
...             [5, 2, 'phylum']], columns=[
...     'tax_id', 'parent_tax_id', 'rank']).set_index('tax_id')
>>> names = {1: 'root', 2: 'Bacteria', 3: 'Archaea',
...          4: 'Firmicutes', 5: 'Bacteroidetes'}
>>> tree = TreeNode.from_taxdump(nodes, names)
>>> print(tree.ascii_art())
                    /-Firmicutes
          /Bacteria|
-root----|          \-Bacteroidetes
         |
          \-Archaea