def generate_skbio_tree(classification, existing_tree=None):
from skbio.tree import MissingNodeError, TreeNode
otus = classification.results()['table']
if existing_tree is None:
tree = TreeNode(name='1', length=1)
tree.tax_name = 'Root'
tree.rank = 'no rank'
else:
tree = existing_tree
# we use this to keep track of nodes that haven't had their parent added yet
unlinked = defaultdict(list)
for otu in otus:
tax_id = otu['tax_id']
# skip nodes already in the tree
try:
tree.find(tax_id)
continue
except MissingNodeError:
pass
# try to find a parent (if it exists)
parent_id = otu['parent_tax_id']
try:
parent = tree.find(parent_id)
# the children are merged out here (only if we have a parent) to
# make sure we're not creating trees inside unlinked itself
children = _merge_unlinked(tax_id, unlinked)
except MissingNodeError:
parent = None
children = None
# create the node
node = TreeNode(name=tax_id, length=1, children=children)
node.tax_name = otu.get('name', '')
node.rank = otu.get('rank', 'no rank')
# either add the node to its parent or keep track of it until its
# parent is "in tree" too
if parent is not None:
parent.append(node)
else:
unlinked[parent_id].append(node)
assert len(
unlinked) == 0, 'some unlinked nodes were not included in the tree'
return tree
def tree_build(self):
"""Build a tree from the taxonomy data present in this object.
This is designed for use with `ClassificationsDataFrame` or `SampleCollection`.
Returns
-------
`skbio.tree.TreeNode`, the root node of a tree that contains all the taxa in the current
analysis and their parents leading back to the root node.
"""
from skbio.tree import TreeNode
# build all the nodes
nodes = {}
for tax_id in self.taxonomy.index:
node = TreeNode(name=tax_id, length=1)
node.tax_name = self.taxonomy["name"][tax_id]
node.rank = self.taxonomy["rank"][tax_id]
node.parent_tax_id = self.taxonomy["parent_tax_id"][tax_id]
nodes[tax_id] = node
# generate all the links
for tax_id in self.taxonomy.index:
try:
parent = nodes[nodes[tax_id].parent_tax_id]
except KeyError:
if tax_id != "1":
warnings.warn(
"tax_id={} has parent_tax_id={} which is not in tree"
"".format(tax_id, nodes[tax_id].parent_tax_id))
continue
parent.append(nodes[tax_id])
return nodes["1"]
def tree_build(self):
"""Build a tree from the taxonomy data present in this `ClassificationsDataFrame` or
`SampleCollection`.
Returns
-------
`skbio.tree.TreeNode`, the root node of a tree that contains all the taxa in the current
analysis and their parents leading back to the root node.
"""
from skbio.tree import TreeNode
# build all the nodes
nodes = {}
for tax_id in self.taxonomy.index:
node = TreeNode(name=tax_id, length=1)
node.tax_name = self.taxonomy["name"][tax_id]
node.rank = self.taxonomy["rank"][tax_id]
node.parent_tax_id = self.taxonomy["parent_tax_id"][tax_id]
nodes[tax_id] = node
# generate all the links
for tax_id in self.taxonomy.index:
try:
parent = nodes[nodes[tax_id].parent_tax_id]
except KeyError:
if tax_id != "1":
warnings.warn(
"tax_id={} has parent_tax_id={} which is not in tree"
"".format(tax_id, nodes[tax_id].parent_tax_id)
)
continue
parent.append(nodes[tax_id])
return nodes["1"]