def test_recursivekinship():
peds = getpeds()
ped = peds['fullsib']
# Self
assert ped.kinship('1', '1') == 1/2
# Unrelated founders
assert ped.kinship('1', '2') == 0
# Full-sib
assert ped.kinship('3', '4') == 1/4
# Parent-child
assert ped.kinship('1', '3') == 1/4
ped = peds['first_cousins']
# First cousins
assert ped.kinship('7', '8') == 1/16
# Avuncular (related)
assert ped.kinship('7', '5') == 1/8
# Avuncular (marry-in)
assert ped.kinship('7', '6') == 0
# Grandparent
assert ped.kinship('7', '1') == 1/8
ped = peds['half_sibs']
assert ped.kinship('4', '5') == 1/8
def test_pathfraternity():
from pydigree.paths import fraternity
peds = getpeds()
ped = peds["fullsib"]
# None should return 0
assert fraternity(ped["1"], None) == 0
# Unrelated founders
assert fraternity(ped["1"], ped["2"]) == 0
# Full-sib
assert fraternity(ped["3"], ped["4"]) == 1 / 4
# Parent-child
assert fraternity(ped["1"], ped["3"]) == 0
ped = peds["first_cousins"]
# First cousins
assert fraternity(ped["7"], ped["8"]) == 0
# Avuncular (related)
assert fraternity(ped["7"], ped["5"]) == 0
# Avuncular (marry-in)
assert fraternity(ped["7"], ped["6"]) == 0
# Grandparent
assert fraternity(ped["7"], ped["1"]) == 0
ped = peds["half_sibs"]
assert fraternity(ped["4"], ped["5"]) == 0
def test_recursivekinship():
peds = getpeds()
ped = peds['fullsib']
# Self
assert ped.kinship('1', '1') == 1/2
# Unrelated founders
assert ped.kinship('1', '2') == 0
# Full-sib
assert ped.kinship('3', '4') == 1/4
# Parent-child
assert ped.kinship('1', '3') == 1/4
ped = peds['first_cousins']
# First cousins
assert ped.kinship('7', '8') == 1/16
# Avuncular (related)
assert ped.kinship('7', '5') == 1/8
# Avuncular (marry-in)
assert ped.kinship('7', '6') == 0
# Grandparent
assert ped.kinship('7', '1') == 1/8
ped = peds['half_sibs']
assert ped.kinship('4', '5') == 1/8
def test_inbreeding():
peds = getpeds()
ped = peds['first_cousin_child']
assert ped.inbreeding('9') == 1/16
# Everyone else is outbred
for x in ped.individuals:
if x.label == '9':
continue
assert ped.inbreeding(x.label) == 0
def test_inbreeding():
peds = getpeds()
ped = peds['first_cousin_child']
assert ped.inbreeding('9') == 1/16
# Everyone else is outbred
for x in ped.individuals:
if x.label == '9':
continue
assert ped.inbreeding(x.label) == 0
def test_bitsize():
peds = getpeds()
fullsib = peds['fullsib']
assert fullsib.bit_size() == 2
first_cousins = peds['first_cousins']
assert first_cousins.bit_size() == 4
huntingtons = peds['vz_huntington_autosomal_dominant']
assert huntingtons.bit_size() == 2*47-18
def test_bitsize():
peds = getpeds()
fullsib = peds['fullsib']
assert fullsib.bit_size() == 2
first_cousins = peds['first_cousins']
assert first_cousins.bit_size() == 4
huntingtons = peds['vz_huntington_autosomal_dominant']
assert huntingtons.bit_size() == 2*47-18
def test_commonancestors():
from pydigree.paths import common_ancestors
peds = getpeds()
ped = peds["fullsib"]
# Two founders have no common ancestors
assert common_ancestors(ped["1"], ped["2"]) == set()
# Parent and child no common ancestors
assert common_ancestors(ped["1"], ped["3"]) == set()
# Full sibs have parents in common
assert common_ancestors(ped["3"], ped["4"]) == {ped["1"], ped["2"]}
# Test first cousins
ped = peds["first_cousins"]
assert common_ancestors(ped["7"], ped["8"]) == {ped["1"], ped["2"]}
def test_recursivefraternity():
peds = getpeds()
ped = peds['fullsib']
# Unrelated founders
assert ped.fraternity('1', '2') == 0
# Full-sib
assert ped.fraternity('3', '4') == 1/4
# Parent-child
assert ped.fraternity('1', '3') == 0
ped = peds['first_cousins']
# First cousins
assert ped.fraternity('7', '8') == 0
# Avuncular (related)
assert ped.fraternity('7', '5') == 0
# Avuncular (marry-in)
assert ped.fraternity('7', '6') == 0
# Grandparent
assert ped.fraternity('7', '1') == 0
ped = peds['half_sibs']
assert ped.fraternity('4', '5') == 0
def test_recursivefraternity():
peds = getpeds()
ped = peds['fullsib']
# Unrelated founders
assert ped.fraternity('1', '2') == 0
# Full-sib
assert ped.fraternity('3', '4') == 1/4
# Parent-child
assert ped.fraternity('1', '3') == 0
ped = peds['first_cousins']
# First cousins
assert ped.fraternity('7', '8') == 0
# Avuncular (related)
assert ped.fraternity('7', '5') == 0
# Avuncular (marry-in)
assert ped.fraternity('7', '6') == 0
# Grandparent
assert ped.fraternity('7', '1') == 0
ped = peds['half_sibs']
assert ped.fraternity('4', '5') == 0
