Nodes

taxidTools.Node.Node

Bases: _BaseNode

Taxonomic Node

Create a Node object contining taxonomic information as well as a link to parent and children nodes.

Parameters:

• taxid (Union[str, int]) –

  Taxonomic identification number

• name (Optional[str], default: None ) –

  Node name

• rank (Optional[str], default: None ) –

  Node rank

• parent (Optional[_BaseNode], default: None ) –

  The parent Node object

Notes

The children property will be dynamically populated when children Nodes declare a Node as parent.

Attributes:

• taxid (str) –
• name (str) –
• rank (str) –
• children (list) –
• parent (str) –
• node_info (str) –

Examples:

>>> root = Node(1, "root", "root")
>>> child = Node(2, "child", "child_rank", root)

>>> child.taxid
'2'
>>> child.rank
'child_rank'
>>> child.name
'child'

>>> child.parent
Node object:
        Taxid: 1
        Name: root
        Rank: root
        Parent: None

>>> root.children
[Node object:
        Taxid: 2
        Name: child
        Rank: child_rank
        Parent: 1]

children: list property writable

Children nodes

name: str property writable

Name of the taxonomic node

node_info: str property

Node information

parent: str property writable

Parent node

rank: str property writable

Rank of the taxonomic node

taxid: str property writable

Taxonomic identification number

isAncestorOf(node)

Test if the object is an ancestor of another Node.

Parameters:

• node (Node) –

  Putative descendant node

Examples:

>>> root = Node(1, "root", "root")
>>> node = Node(2, "node", "rank", root)
>>> node.isAncestorOf(root)
False
root.isAncestorOf(node)
True

isDescendantOf(node)

Test if the object is an ancestor of another Node.

Parameters:

• node (Node) –

  Putative ancestor node

Examples:

>>> root = Node(1, "root", "root")
>>> node = Node(2, "node", "rank", root)
>>> node.isDescendantOf(root)
True
root.isDescendantOf(node)
False

taxidTools.Node.DummyNode

Bases: _BaseNode

A placeholder for a non-existing Node.

Will be assigned a random hash id in place of a taxid upon creation. Can be inserted between two existing nodes.

Parameters:

• taxid (Optional[Union[str, int]], default: None ) –

  Taxonomic identification number

• name (Optional[str], default: None ) –

  Node name

• rank (Optional[str], default: None ) –

  Node rank

• parent (Optional[_BaseNode], default: None ) –

  The parent Node object

Attributes:

• taxid (str) –
• name (str) –
• rank (str) –
• children (list) –
• parent (str) –
• node_info (str) –

children: list property writable

Children nodes

name: str property writable

Name of the taxonomic node

node_info: str property

Node information

parent: str property writable

Parent node

rank: str property writable

Rank of the taxonomic node

taxid: str property writable

Taxonomic identification number

insertNode(parent, child)

Insert the dummy node between parent and child

Parameters:

• parent (_BaseNode) –

  Upstream node

• child (_BaseNode) –

  Downstream node

Returns:

• None –

isAncestorOf(node)

Test if the object is an ancestor of another Node.

Parameters:

• node (Node) –

  Putative descendant node

Examples:

>>> root = Node(1, "root", "root")
>>> node = Node(2, "node", "rank", root)
>>> node.isAncestorOf(root)
False
root.isAncestorOf(node)
True

isDescendantOf(node)

Test if the object is an ancestor of another Node.

Parameters:

• node (Node) –

  Putative ancestor node

Examples:

>>> root = Node(1, "root", "root")
>>> node = Node(2, "node", "rank", root)
>>> node.isDescendantOf(root)
True
root.isDescendantOf(node)
False

taxidTools.Node.MergedNode

Simple class linking to an instance of (a subclass of) _BaseNode

Represents a taxonomic node that has been merged with another node and is therefore not part of the taxonomy anymore. This is not a subclass of _BaseNode.

Parameters:

• taxid (Union[str, int]) –

  Taxonomic identification number

• new_node (Union[str, int]) –

  Taxid of node this node has been merged with

• *args –

  ignored

• **kwargs –

  ignored

Attributes:

• taxid (str) –
• new_node (str) –

Note

new_node is provided as a taxid and not as an instance of a Node class. An Error will be raised upon trying to access a MergedNode from Taxonomy object if it is linked to a non-existing Node.

new_node: str property writable

Node this node has been merged with

taxid: str property writable

Taxonomic identification number