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