phylox.cherrypicking.base

Functions

`add_pair`(network, x, y[, height, inplace, ...])	Adds a pair to the network, using the construction from a cherry-picking sequence :param x: first element of the pair :param y: second element of the pair :param height: height of the pair :param inplace: if true, the network is modified in place, otherwise a copy is returned :param nodes_by_label: if true, the nodes are indexed by their label, otherwise by their index :return: the network with the pair added
`add_roots_to_sequence`(sequence, ...)	Modifies a cherry-picking sequence so that it represents a network with exactly one root.
`check_reducible_pair`(network, x, y)	Checks whether the pair (x,y) is a reducible pair in the network.
`cherry_height`(network, x, y)	Returns the height of (x,y) if it is a cherry:
`find_all_reducible_pairs`(network)	Finds all reducible pairs (cherries and reticulated cherries) in the network.
`find_cherries_with_first`(network, x)	Finds a set of cherries in the network N with leaf x as first element of the pair.
`find_reducible_pairs_with_first`(N, x)	Finds a list of reducible pairs (cherries and reticulated cherries) in the network N with leaf x as first element of the pair.
`find_reducible_pairs_with_second`(N, x)	Finds a list of reducible pairs (cherries and reticulated cherries) in the network N with leaf x as second element of the pair.
`find_reticulated_cherry_with_first`(N, x)	Finds a list of reticulated cherries in the network N with leaf x as first element of the pair.
`get_indices_of_reducing_pairs`(sequence, network)	Checks which pairs of a sequence actually reduce a given network for a given cherry-picking sequence `sequence' reduces a given tree `tree' input: sequence: a list of pairs of leaves network: a network output: if the network is reduced by the sequence, returns the list of all indices of pairs that reduce the network otherwise returns False
`has_cherry`(network, x, y)	Checks whether the pair (x,y) forms a cherry in the network
`is_second_in_reducible_pair`(network, x)
`reduce_pair`(network, x, y[, inplace, ...])	Reduces the reducible pair (x,y) in the network.

Classes

`CHERRYTYPE`(value[, names, module, qualname, ...])
`CherryPickingMixin`()

class phylox.cherrypicking.base.CHERRYTYPE(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None): Bases: Enum

phylox.cherrypicking.base.find_all_reducible_pairs(network)

Finds all reducible pairs (cherries and reticulated cherries) in the network.

Parameters:: network – a phylogenetic network.
Returns:: a set of reducible pairs (cherries and reticulated cherries) in the network.
Example:

>>> from phylox import DiNetwork
>>> from phylox.cherrypicking.base import find_all_reducible_pairs
>>> network = DiNetwork(
...     edges=[(-1,0),(0,1),(1,2),(1,3),(2,3),(2,4),(3,5),(0,6),(6,7),(6,8)],
... )
>>> reducible_pairs = find_all_reducible_pairs(network)
>>> reducible_pairs == {(7,8),(8,7),(5,4)}
True

phylox.cherrypicking.base.find_reducible_pairs_with_second(N, x)

Finds a list of reducible pairs (cherries and reticulated cherries) in the network N with leaf x as second element of the pair.

Parameters:

N – a phylogenetic network.
x – a leaf of the network N.

Returns:

a list of reducible pairs (cherries and reticulated cherries) in the network N with leaf x as second element of the pair.

Example:

>>> from phylox import DiNetwork
>>> from phylox.cherrypicking.base import find_reducible_pairs_with_second
>>> network = DiNetwork(
...     edges=[(-1,0), (0,1), (0,2), (1,2), (1,3), (2,4)],
... )
>>> find_reducible_pairs_with_second(network, 3)
[(4, 3)]

phylox.cherrypicking.base.find_reducible_pairs_with_first(N, x)

Finds a list of reducible pairs (cherries and reticulated cherries) in the network N with leaf x as first element of the pair.

Parameters:

N – a phylogenetic network.
x – a leaf of the network N.

Returns:

a list of reducible pairs (cherries and reticulated cherries) in the network N with leaf x as first element of the pair.

Example:

>>> from phylox import DiNetwork
>>> from phylox.cherrypicking.base import find_reducible_pairs_with_first
>>> network = DiNetwork(
...     edges=[(-1,0), (0,1), (0,2), (1,2), (1,3), (2,4)],
... )
>>> find_reducible_pairs_with_first(network, 4)
[(4, 3)]

phylox.cherrypicking.base.find_reticulated_cherry_with_first(N, x)

Finds a list of reticulated cherries in the network N with leaf x as first element of the pair.

Parameters:

N (phylox.DiNetwork) – The network to find reticulated cherries in.
x (str or int) – The leaf to find reticulated cherries with.

Returns:

A list of reticulated cherries in the network with leaf x as first element of the pair.

Return type:

list

phylox.cherrypicking.base.find_cherries_with_first(network, x)

Finds a set of cherries in the network N with leaf x as first element of the pair.

Parameters:

network (phylox.DiNetwork) – The network to find cherries in.
x (str or int) – The leaf to find cherries with.

Returns:

A set of cherries in the network with leaf x as first element of the pair.

Return type:

set

phylox.cherrypicking.base.reduce_pair(network, x, y, inplace=False, nodes_by_label=False)

Reduces the reducible pair (x,y) in the network. Note: Cache of network properties is not updated.

Parameters:

network (phylox.DiNetwork) – The network to reduce the reducible pair in.
x (str or int) – The first element of the reducible pair.
y (str or int) – The second element of the reducible pair.
inplace (bool) – If True, the network is modified in place.
nodes_by_label (bool) – If True, the nodes x and y are interpreted as labels.

Returns:

phylox.DiNetwork – The network with the reducible pair reduced.
CHERRYTYPE – The type of the reducible pair.

Raises:

ValueError – If x or y are not in the network.

Examples

>>> from phylox import DiNetwork
>>> from phylox.cherrypicking.base import reduce_pair, CHERRYTYPE
>>> network = DiNetwork(
...     edges=[(-1,0), (0,1), (0,2), (1,2), (1,3), (2,4)],
... )
>>> network, cherry_type = reduce_pair(network, 4, 3)
>>> cherry_type == CHERRYTYPE.RETICULATEDCHERRY
True
>>> set(network.edges) == {(-1, 0), (0, 3), (0, 4)}
True

phylox.cherrypicking.base.check_reducible_pair(network, x, y)

Checks whether the pair (x,y) is a reducible pair in the network.

Parameters:

network – a phylogenetic network.
x – a leaf of the network.
y – a leaf of the network.

Returns:

the type of reducible pair (x,y) in the network.

Example:

>>> from phylox import DiNetwork
>>> from phylox.cherrypicking.base import check_reducible_pair, CHERRYTYPE
>>> network = DiNetwork(
...     edges=[(-1,0), (0,1), (0,2), (1,2), (1,3), (2,4)],
... )
>>> check_reducible_pair(network, 4, 3) == CHERRYTYPE.RETICULATEDCHERRY
True

phylox.cherrypicking.base.add_pair(network, x, y, height=[1, 1], inplace=False, nodes_by_label=False): Adds a pair to the network, using the construction from a cherry-picking sequence :param x: first element of the pair :param y: second element of the pair :param height: height of the pair :param inplace: if true, the network is modified in place, otherwise a copy is returned :param nodes_by_label: if true, the nodes are indexed by their label, otherwise by their index :return: the network with the pair added

phylox.cherrypicking.base.get_indices_of_reducing_pairs(sequence, network)

Checks which pairs of a sequence actually reduce a given network for a given cherry-picking sequence `sequence’ reduces a given tree `tree’ input:

sequence: a list of pairs of leaves network: a network

output:: if the network is reduced by the sequence, returns the list of all indices of pairs that reduce the network otherwise returns False

phylox.cherrypicking.base.add_roots_to_sequence(sequence, reduced_trees_per_pair)

Modifies a cherry-picking sequence so that it represents a network with exactly one root. A sequence may be such that reconstructing a network from the sequence results in multiple roots This function adds some pairs to the sequence so that the network has a single root. :param sequence: the sequence to modify :param reduced_trees_per_pair: the sets of trees reduced by each pair in the sequence

Returns:: the new sequence, and also the sets of trees reduced by each pair in the sequence, modified so that the new pairs are also represented (they reduce no trees)

phylox.cherrypicking.base.has_cherry(network, x, y)

Checks whether the pair (x,y) forms a cherry in the network

Parameters:

network (phylox.DiNetwork) – The network in which we want to check whether (x,y) is a cherry
x (string) – The first element of the pair
y (string) – The second element of the pair

Returns:

True if (x,y) is a cherry in the network, False otherwise

Return type:

bool

phylox.cherrypicking.base.cherry_height(network, x, y)

Returns the height of (x,y) if it is a cherry:: i.e.: length(p,x)+length(p,y)/2

Returns false otherwise

Parameters:

network (phylox.DiNetwork) – The network in which we want to check the height of cherry (x,y)
x (string) – The first element of the pair
y (string) – The second element of the pair

Returns:

The height of the cherry (x,y) if it is a cherry, False otherwise

Return type:

float