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 property writable

Children nodes

name property writable

Name of the taxonomic node

node_info property

Node information

parent property writable

Parent node

rank property writable

Rank of the taxonomic node

taxid 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 property writable

Children nodes

name property writable

Name of the taxonomic node

node_info property

Node information

parent property writable

Parent node

rank property writable

Rank of the taxonomic node

taxid 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 property writable

Node this node has been merged with

taxid property writable

Taxonomic identification number