pydigree.simulation.genedrop package

Submodules

pydigree.simulation.genedrop.constrained_mendelian module

Genedropping with IBD constraints

class pydigree.simulation.genedrop.constrained_mendelian.ConstrainedMendelianSimulation(template=None, label=None, replications=1000, only=None)

Bases: pydigree.simulation.genedrop.simulation.GeneDroppingSimulation

Performs a gene-dropping simulation constrained to a specific IBD pattern

replicate(writeibd=False, verbose=False, replicatenumber=0)

Creates a replicate from the simulation

pydigree.simulation.genedrop.naivegenedrop module

Naive gene dropping simulations

class pydigree.simulation.genedrop.naivegenedrop.NaiveGeneDroppingSimulation(template=None, replications=1000)

Bases: pydigree.simulation.genedrop.simulation.GeneDroppingSimulation

A class that performs simulations on pedigrees by randomly segregating chromosome through the pedigree

replicate(writeibd=False, verbose=None, replicatenumber=0)

Perform a single replicate of gene-dropping

Parameters:

• writeibd (bool) – write IBD states?
• verbose (bool) – print incremental output
• replicatenumber (int) – current replicate

Return type:

void

pydigree.simulation.genedrop.simulation module

A base class for gene dropping simulations to inherit from

class pydigree.simulation.genedrop.simulation.GeneDroppingSimulation(template=None, label=None, replications=1000, only=None)

Bases: object

A base class for gene dropping simulations to inherit from

add_founder_genotype_hook(func)

add_genotype_constraint(ind, location, allele, chromatid, method='set')

add_ibd_constraint(ind, ancestor, location, anchap)

get_founder_genotypes(linkeq=True)

predicted_trait_accuracy(ped)

read_constraints(filename)

replicate(**kwargs)

run(verbose=False, writeibd=False, output_predicate=None, compression=None, output_chromosomes=None)

run_founder_genotype_hooks()

set_trait(architecture)

write_data(replicatenumber, predicate=None, compression=None, output_chromosomes=None)

Module contents

Classes for performing gene-dropping simulations in pedigrees