pedigree_tools

pedigree_tools is a python package containing useful methods for working with msprime pedigrees. For now, it is meant to be installed by placing it in your working directory and using import pedigree_tools in your python script. Features include:

• generate_pedigree(num_probands=None, population_size=None, end_time=None, num_pedigrees=None, random_seed=None):
  Generates one or more pedigrees with the specified number of probands, out of a population with the specified size, going back end_time generations.
• get_proband_genealogy(pedigree, chosen_probands):
  Returns a pedigreee trimmed to only the ancestors of the chosen probands.
• get_descendents_genealogy(pedigree, ancestral_individuals):
  Finds the proband descendents of the chosen ancestors, and returns a pedigree trimmed to the ancestors of those probands
• predict_contributions_coalescences(pedigree):
  Predicts the expected genetic contribution of each individual to the probands, as well as the expected rate of coalescence in each individual.