ped

Below is an auto-generated summary of the xftsim.ped submodule API.

class xftsim.ped.Pedigree(founder_samples)

Bases: object

A class representing a pedigree as a graph.

G

The directed graph representing the pedigree.

Type:

nx.DiGraph

_generation

A dictionary containing node generations.

Type:

dict

_fid

A dictionary containing node family IDs.

Type:

dict

_generational_depth

The generational depth of the tree.

Type:

int

generation(K: int):

Returns the subgraph of nodes with generation K.

generations(gens):

Returns the subgraph of nodes with generations in the given iterable.

current_generation(K):

Returns the subgraph of nodes in the current generation.

most_recent_K_generations():

Returns the subgraph of nodes in the most recent K generations.

_add_edges_from_arrays(x, y):

Adds edges from arrays x and y.

add_offspring(mating: xft.mate.MateAssignment):

Adds offspring nodes and edges to the pedigree based on a MateAssignment object.

_get_trios():

TODO

Parameters:

founder_samples (SampleMeta)

property generational_depth

generation(K)

Returns the subgraph of nodes with generation K.

Parameters:

K (int) – The generation number.

Returns:

nx.subgraph_view – The subgraph of nodes with generation K.

Parameters:

K (int)

generations(gens)

Returns the subgraph of nodes with generations in the given iterable.

Parameters:

gens (iterable) – An iterable containing generations.

Returns:

nx.subgraph_view – The subgraph of nodes with generations in the given iterable.

get_current_generation()

Returns the subgraph of nodes in the current generation.

Parameters:

K (int) – The generation number.

Returns:

nx.subgraph_view – The subgraph of nodes in the current generation.

get_most_recent_K_generations(K)

Returns the subgraph of nodes in the most recent K generations.

Returns:

nx.subgraph_view – The subgraph of nodes in the most recent K generations.