Calculating ascending genealogy

All the classes extending from GenGraph have functionality for calculating the ascending graph for a given set of vertices. In general, it works like this:

# Ask the user to specify the path to the pedigree
genealogy_path = input("Specify the path to the genealogy file: ")
# Parse the file
genealogy_graph = GenGraph.get_graph_from_file(filepath=genealogy_path)
# Specify the list of probands
probands = [1, 2, 3, 5, 8, 13, 21, 34, 55, 89, 144]
# Calculate the vertices in the ascending graph. This operation does not modify the graph
vertices_in_ascending_graph = genealogy_graph.get_ascending_vertices_from_probands(probands=probands)
# Remove all the vertices that are not in the ascending graph
genealogy_graph.reduce_to_ascending_graph(probands=probands)

For instance, we can find this function useful when we work with the BALSAC dataset, but we’re only interested in the Cartegene individuals:

# Specify the path
balsac_path = input("Specify the path to BALSAC: ")
# Parse the BALSAC dataset
balsac_pedigree = GenGraph.get_graph_from_file(filepath=balsac_path)
# Get the list of Cartgene participants
cartegene_participants = # Getting the cartegene individuals ... #
# Remove all the vertices that are not present in the ascending pedigree of the Cartegene individuals
balsac_pedigree.reduce_to_ascending_graph(probands=cartegene_participants)

Another example can involve a coalescent tree. Suppose that we want to sub-select a given list of probands in the tree and work with the result. We can use the reduce_to_ascending_graph function in GenGraph and remove_unary_nodes function in CoalescentTree to achieve this.

# Specify the path to the coalescent tree
tree_path = input("Specify the path to the genealogy file: ")
# Parse the coalescent tree
coalescent_tree = CoalescentTree.get_coalescent_tree_from_file(filepath=tree_path)
# Get the list of probands
probands = [1, 2, 4, 11, 34, 156, 1044, 12346, 274668, 12005168]
# Remove all the vertices that are not in the ascending tree
coalescent_tree.reduce_to_ascending_graph(probands=probands)
# After reduction, the tree may contain unary nodes, which are nodes with only a single child.
# We remove these vertices here
coalescent_tree.remove_unary_nodes()