historydag.HistoryDagNode

class historydag.HistoryDagNode(label, clades, attr)[source]

A recursive representation of a history DAG object.

a dictionary keyed by clades (frozensets) containing EdgeSet objects
a label, which is a namedtuple.

__init__(label, clades, attr)[source]

Methods

`__init__`(label, clades, attr)
`add_edge`(target[, weight, prob, prob_norm])	Adds edge, if allowed and not already present.
`child_clades`()	Returns the node's child clades, or a frozenset containing a frozenset if this node is a UANode.
`children`([clade])	Returns generator object containing child nodes.
`clade_union`()	Returns the union of this node's child clades (or a set containing only the node label, for leaf nodes.)
`empty_copy`()	Returns a HistoryDagNode object with the same clades, label, and attr dictionary, but no descendant edges.
`is_history_root`()	Return whether node is a root of any histories in the DAG.
`is_leaf`()	Returns whether this is a leaf node.
`is_root`()	Deprecated name for `is_ua_node()`
`is_ua_node`()	Returns whether this is the source node in the DAG, from which all others are reachable.
`node_self`()	Deprecated name for `empty_copy()`
`partitions`()	Deprecated name for `child_clades()`
`remove_edge_by_clade_and_id`(target, clade)
`remove_node`([nodedict])	Recursively removes node self and any orphaned children from dag.
`sorted_child_clades`()	Returns the node's child clades as a sorted tuple containing leaf labels in sorted tuples.
`sorted_partitions`()	Deprecated name for `sorted_child_clades()`
`to_ascii`(name_func[, show_internal, ...])	A convenience function that uses the `to_ete()` method and ete3's ASCII drawing tools to render a sub-history below self.
`to_ete`([name_func, feature_funcs, sort_func])	Convert a history DAG node which is part of a history to an ete tree.
`under_clade`()	Deprecated name for `clade_union()`

__init__(label, clades, attr)[source]

empty_copy()[source]

Returns a HistoryDagNode object with the same clades, label, and attr dictionary, but no descendant edges.

Return type:: HistoryDagNode

node_self()[source]

Deprecated name for empty_copy()

Return type:: HistoryDagNode

clade_union()[source]

Returns the union of this node’s child clades (or a set containing only the node label, for leaf nodes.)

Return type:: FrozenSet[Union[NamedTuple, UALabel]]

under_clade()[source]

Deprecated name for clade_union()

Return type:: FrozenSet[Union[NamedTuple, UALabel]]

is_leaf()[source]

Returns whether this is a leaf node.

Return type:: bool

is_ua_node()[source]

Returns whether this is the source node in the DAG, from which all others are reachable.

Return type:: bool

is_root()[source]

Deprecated name for is_ua_node()

Return type:: bool

is_history_root()[source]

Return whether node is a root of any histories in the DAG.

Return type:: bool

child_clades()[source]

Returns the node’s child clades, or a frozenset containing a frozenset if this node is a UANode.

Return type:: frozenset

partitions()[source]

Deprecated name for child_clades()

Return type:: frozenset

sorted_child_clades()[source]

Returns the node’s child clades as a sorted tuple containing leaf labels in sorted tuples.

Return type:: tuple

sorted_partitions()[source]

Deprecated name for sorted_child_clades()

Return type:: tuple

children(clade=None)[source]

Returns generator object containing child nodes.

Parameters:: clade (Optional[Set[Union[NamedTuple, UALabel]]]) – If clade is provided, returns generator object of edge targets from that
Return type:: Generator[HistoryDagNode, None, None]

clade. If no clade is provided, generator includes all children of self.

add_edge(target, weight=0, prob=None, prob_norm=True)[source]

Adds edge, if allowed and not already present.

Returns whether edge was added.

Return type:: bool

remove_node(nodedict={})[source]

Recursively removes node self and any orphaned children from dag.

May not work on root. Does not check to make sure that parent clade still has descendant edges.

to_ascii(name_func, show_internal=False, compact=False, sort_method=None)[source]

A convenience function that uses the to_ete() method and ete3’s ASCII drawing tools to render a sub-history below self.

Expects that this node is part of a tree-shaped history DAG. If this is not true, this method may fail silently.

Parameters:

name_func – A function taking a HistoryDagNode and returning a string to identify that node in the ascii tree.
show_internal – Whether to show internal node names.
compact – Whether to show the tree in a more compact format
sort_method – Either None, ladderize, leaf-name, or child-name. leaf-name sorts children by the alphabetically first leaf name below each child node. child-name sorts directly by child name.

Returns:

A string including whitespace and newlines (no tabs) which when printed shows the structure of the history.

to_ete(name_func=lambda n: ..., feature_funcs={}, sort_func=lambda seq: ...)[source]

Convert a history DAG node which is part of a history to an ete tree.

Parameters:

name_func (Callable[[HistoryDagNode], str]) – A map from nodes to newick node names
feature_funcs (Mapping[str, Callable[[HistoryDagNode], str]]) – A dictionary keyed by extended newick field names, containing functions specifying how to populate that field for each node.

Return type:

TreeNode

Returns:

An ete3 Tree with the same topology as the subhistory below self, and node names and attributes as specified.