phylox.rearrangement.move

Functions

`all_valid_moves`(network[, move_type])	Generates all possible valid moves for a given network and move type.
`apply_move`(network, move)	Apply a move to the network, not in place.
`apply_move_sequence`(network, seq_moves)	Apply a sequence of moves to the network, not in place.

Classes

Move(*args, **kwargs)

A move is a rearrangement operation on a phylogenetic network.

phylox.rearrangement.move.apply_move(network, move)

Apply a move to the network, not in place. returns True if successful, and False otherwise.

Parameters:

network – a phylogenetic network (phylox.DiNetwork).
move – a move (phylox.rearrangement.move.Move) to apply to the network.

Returns:

a new phylogenetic network (phylox.DiNetwork) with the move applied.

Example:

>>> from phylox import DiNetwork
>>> from phylox.rearrangement.move import apply_move, Move
>>> network = DiNetwork(
...     edges=[(0,1),(1,2),(1,3),(2,3),(2,4),(3,5)],
... )
>>> move = Move(
...     move_type=MoveType.HEAD,
...     origin=(2,5),
...     moving_edge=(1,3),
...     target=(2,4),
... )
>>> new_network = apply_move(network, move)
>>> edges = set(new_network.edges())
>>> edges == {(0, 1), (1, 2), (1, 3), (2, 3), (3, 4), (2, 5)}
True

phylox.rearrangement.move.apply_move_sequence(network, seq_moves)

Apply a sequence of moves to the network, not in place. returns the resulting network.

Parameters:

network – a phylogenetic network (phylox.DiNetwork).
seq_moves – a sequence of moves (list of phylox.rearrangement.move.Move) to apply to the network.

Returns:

a new phylogenetic network (phylox.DiNetwork) with the moves applied.

Example:

>>> from phylox import DiNetwork
>>> from phylox.rearrangement.move import apply_move_sequence, Move
>>> network = DiNetwork(
...     edges=[(0,1),(1,2),(1,3),(2,4),(2,5),(3,6),(3,7)],
... )
>>> seq_moves = [
...     Move(
...         move_type=MoveType.TAIL,
...         moving_edge=(3,6),
...         target=(0,1),
...         origin=(1,7),
...     ),
...     Move(
...         move_type=MoveType.VPLU,
...         start_edge=(1,2),
...         end_edge=(1,7),
...         network=network,
...     ),
... ]
>>> new_network = apply_move_sequence(network, seq_moves)
>>> edges = set(new_network.edges())
>>> edges == {(0, 3), (3, 1), (1, -1), (-1, 2), (1, -2), (-2, 7), (2, 4), (2, 5), (3, 6), (-1, -2)}
True

phylox.rearrangement.move.all_valid_moves(network, move_type=MoveType.ALL)

Generates all possible valid moves for a given network and move type.

Parameters:

network – a phylogenetic network (phylox.DiNetwork).
move_type – the type of moves to generate (phylox.rearrangement.movetype.MoveType).

Yield:

a move (phylox.rearrangement.move.Move).

Example:

>>> from phylox import DiNetwork
>>> from phylox.rearrangement.move import all_valid_moves
>>> network = DiNetwork(
...     edges=[(0,1),(1,2),(1,3)],
... )
>>> moves = list(all_valid_moves(network, MoveType.TAIL))
>>> len(moves)
4
>>> moves[0].is_type(MoveType.TAIL)
True
>>> moves = list(all_valid_moves(network, MoveType.VERT))
>>> len(moves)
4
>>> moves[0].is_type(MoveType.VPLU)
True

class phylox.rearrangement.move.Move(*args, **kwargs)

Bases: object

A move is a rearrangement operation on a phylogenetic network.

Parameters:

move_type – the type of move (phylox.rearrangement.movetype.MoveType).
kwargs – the parameters of the move, depending on the move type.

is_type(move_type)

Checks if the move is of a given type.

Parameters:: move_type – the move type to check (phylox.rearrangement.movetype.MoveType).
Returns:: True if the move is of the given type, False otherwise.
Example:

>>> from phylox.rearrangement.move import Move
>>> move = Move(
...     move_type=MoveType.TAIL,
...     origin=(2,5),
...     moving_edge=(1,3),
...     target=(2,4),
... )
>>> move.is_type(MoveType.TAIL)
True
>>> move.is_type(MoveType.RSPR)
True
>>> move.is_type(MoveType.HEAD)
False
>>> move.is_type(MoveType.VERT)
False

rename_nodes(isomorphism)

Renames the nodes in the move using an isomorphism mapping between two networks.

Parameters:: isomorphism – a dictionary, containing a bijective mapping from nodes of the networks to another set.
Returns:: a new move with the nodes renamed.

invert(network=None)

Inverts the move.

Parameters:: network – a phylogenetic network (phylox.DiNetwork) in which to invert the move. (needed for VMIN moves)
Returns:: a new move that is the inverse of the current move.

classmethod random_move(network, available_tree_nodes=None, available_reticulations=None, move_type_probabilities={MoveType.HEAD: 0.4, MoveType.TAIL: 0.4, MoveType.VMIN: 0.1, MoveType.VPLU: 0.1}, seed=None)

Generates a random move for the given network. The move may not be valid.

Parameters:

network – a phylogenetic network (phylox.DiNetwork).
available_tree_nodes – a list of available tree nodes to use for the move.
available_reticulations – a list of available reticulations to use for the move.
move_type_probabilities – a dictionary of move type probabilities.

Returns:

a random move (phylox.rearrangement.move.Move).

Example:

>>> from phylox import DiNetwork
>>> from phylox.rearrangement.move import Move
>>> network = DiNetwork(
...     edges=[(0,1),(1,2),(1,3),(2,3),(2,4),(3,5)],
... )
>>> move = Move.random_move(
...     network,
...     move_type_probabilities={
...         MoveType.TAIL: 0.5,
...         MoveType.HEAD: 0.5,
...     },
... )
>>> move.is_type(MoveType.RSPR)
True