def test_distant():
p = Ped(op.join(HERE, 'peddy/tests/test-unknown-gma.ped'))
d = p.relatedness_coefficient('kid1', 'cousin1')
assert d == 0.125, d
d = p.relatedness_coefficient('kid1', 'aunt')
assert d == 0.25, d
d = p.relatedness_coefficient('cousin1', 'aunt')
assert d == 0.5, d
d = p.relatedness_coefficient('mom', 'aunt')
assert d == 0.5, d
r = p.relation('kid1', 'cousin1')
assert r == 'cousins', r
r = p.relation('kid1', 'grandma')
assert r == 'grandchild', r
r = p.relation('kid1', 'aunt')
assert r == 'niece/nephew', r
# because we don't know that the uncle is related
r = p.relation('kid1', 'uncle')
assert r == 'related at unknown level', r
r = p.relation('cousin1', 'mom')
assert r == 'niece/nephew', r
r = p.relation('cousin1', 'dad')
# because we don't know that the dad is related
assert r == 'related at unknown level', r
def test_relatedness_coefficient_missing_parent():
gma = Sample('X28935', 'gma', '-9', '-9', '2', '1')
mom = Sample('X28935', 'mom', '-9', 'gma', '2', '1')
dad = Sample('X28935', 'dad', '-9', '-9', '1', '1')
kid1 = Sample('X28935', 'kid1', '-9', 'mom', '1', '1')
kid2 = Sample('X28935', 'kid2', '-9', 'mom', '2', '1')
kid1 = Sample('X28935', 'kid1', 'dad', 'mom', '1', '1')
kid2 = Sample('X28935', 'kid2', 'dad', 'mom', '2', '1')
kid1.mom = mom
kid2.mom = mom
mom.mom = gma
kid1.dad = dad
kid2.dad = dad
from io import StringIO
p = Ped(StringIO())
p.families['X28935'] = Family([kid1, kid2, mom, gma]) #, dad])
assert "siblings" in p.relation('kid1', 'kid2'), p.relation('kid1', 'kid2')
v = p.relatedness_coefficient('kid1', 'kid2')
assert v == 0.5, v
v = p.relatedness_coefficient('gma', 'kid2')
assert v == 0.25, v
v = p.relatedness_coefficient('gma', 'kid1')
assert v == 0.25, v
v = p.relatedness_coefficient('gma', 'mom')
assert v == 0.5, v
def test_distant():
p = Ped(op.join(HERE, 'peddy/tests/test-unknown-gma.ped'))
d = p.relatedness_coefficient('kid1', 'cousin1')
assert d == 0.125, d
d = p.relatedness_coefficient('kid1', 'aunt')
assert d == 0.25, d
d = p.relatedness_coefficient('cousin1', 'aunt')
assert d == 0.5, d
d = p.relatedness_coefficient('mom', 'aunt')
assert d == 0.5, d
r = p.relation('kid1', 'cousin1')
assert r == 'cousins', r
r = p.relation('kid1', 'grandma')
assert r == 'grandchild', r
r = p.relation('kid1', 'aunt')
assert r == 'niece/nephew', r
# because we don't know that the uncle is related
r = p.relation('kid1', 'uncle')
assert r == 'related at unknown level', r
r = p.relation('cousin1', 'mom')
assert r == 'niece/nephew', r
r = p.relation('cousin1', 'dad')
# because we don't know that the dad is related
assert r == 'related at unknown level', r
def test_relatedness_coefficient_missing_parent():
gma = Sample('X28935', 'gma', '-9', '-9', '2', '1')
mom = Sample('X28935', 'mom', '-9', 'gma', '2', '1')
dad = Sample('X28935', 'dad', '-9', '-9', '1', '1')
kid1 = Sample('X28935', 'kid1', '-9', 'mom', '1', '1')
kid2 = Sample('X28935', 'kid2', '-9', 'mom', '2', '1')
kid1 = Sample('X28935', 'kid1', 'dad', 'mom', '1', '1')
kid2 = Sample('X28935', 'kid2', 'dad', 'mom', '2', '1')
kid1.mom = mom
kid2.mom = mom
mom.mom = gma
kid1.dad = dad
kid2.dad = dad
from io import StringIO
p = Ped(StringIO())
p.families['X28935'] = Family([kid1, kid2, mom, gma])#, dad])
assert "siblings" in p.relation('kid1', 'kid2'), p.relation('kid1', 'kid2')
v = p.relatedness_coefficient('kid1', 'kid2')
assert v == 0.5, v
v = p.relatedness_coefficient('gma', 'kid2')
assert v == 0.25, v
v = p.relatedness_coefficient('gma', 'kid1')
assert v == 0.25, v
v = p.relatedness_coefficient('gma', 'mom')
assert v == 0.5, v
def test_relatedness_coefficient():
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
dad = Sample('fam1', 'dad', '-9', '-9', '1', '2')
mom = Sample('fam1', 'mom', '-9', '-9', '2', '2')
gma = Sample('fam1', 'gma', '-9', '-9', '2', '2')
ggma = Sample('fam1', 'ggma', '-9', '-9', '2', '2')
kid.mom = mom
kid.dad = dad
mom.mom = gma
gma.mom = ggma
unrelated = Sample('fam1', 'un', '-9', '-9', '2', '2')
from io import StringIO
p = Ped(StringIO())
p.families['fam1'] = Family([kid, mom, dad, gma, ggma, unrelated])
rel = p.relatedness_coefficient("mom", "dad")
assert rel == 0.0, rel
d = p.relatedness_coefficient("mom", "kid")
assert d == 0.5, d
d = p.relatedness_coefficient("dad", "gma")
assert d == 0.0, d
d = p.relatedness_coefficient("mom", "gma")
assert d == 0.5, d
d = p.relatedness_coefficient("kid", "gma")
assert d == 0.25, d
d = p.relatedness_coefficient("kid", "ggma")
assert d == 0.125, d
assert p.relatedness_coefficient("mom", "mom") == 1.0
def test_relatedness_coefficient():
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
dad = Sample('fam1', 'dad', '-9', '-9', '1', '2')
mom = Sample('fam1', 'mom', '-9', '-9', '2', '2')
gma = Sample('fam1', 'gma', '-9', '-9', '2', '2')
ggma = Sample('fam1', 'ggma', '-9', '-9', '2', '2')
kid.mom = mom
kid.dad = dad
mom.mom = gma
gma.mom = ggma
unrelated = Sample('fam1', 'un', '-9', '-9', '2', '2')
from io import StringIO
p = Ped(StringIO())
p.families['fam1'] = Family([kid, mom, dad, gma, ggma, unrelated])
rel = p.relatedness_coefficient("mom", "dad")
assert rel == 0.0, rel
d = p.relatedness_coefficient("mom", "kid")
assert d == 0.5, d
d = p.relatedness_coefficient("dad", "gma")
assert d == 0.0, d
d = p.relatedness_coefficient("mom", "gma")
assert d == 0.5, d
d = p.relatedness_coefficient("kid", "gma")
assert d == 0.25, d
d = p.relatedness_coefficient("kid", "ggma")
assert d == 0.125, d
assert p.relatedness_coefficient("mom", "mom") == 1.0
def test_relatedness_coefficient_missing_gparent():
p = Ped(open(os.path.join(HERE, "peddy/tests/test.fam.ped")))
# uncle
v = p.relatedness_coefficient('101806-101806', '101811-101811')
assert v == 0.25, v
v = p.relatedness_coefficient('101806-101806', '101809-101809')
assert v == 0.25, v
# parent-child
v = p.relatedness_coefficient('101806-101806', '101653-101653')
assert v == 0.5, v
p = Ped(open(os.path.join(HERE, "peddy/tests/test.fam2.ped")))
v = p.relatedness_coefficient('101806-101806', '101811-101811')
assert v == 0.25, v
v = p.relatedness_coefficient('101806-101806', '101809-101809')
assert v == 0.25, v
# parent-child
v = p.relatedness_coefficient('101806-101806', '101653-101653')
assert v == 0.5, v
def test_relatedness_coefficient_missing_gparent():
p = Ped(open(os.path.join(HERE, "peddy/tests/test.fam.ped")))
# uncle
v = p.relatedness_coefficient('101806-101806', '101811-101811')
assert v == 0.25, v
v = p.relatedness_coefficient('101806-101806', '101809-101809')
assert v == 0.25, v
# parent-child
v = p.relatedness_coefficient('101806-101806', '101653-101653')
assert v == 0.5, v
p = Ped(open(os.path.join(HERE, "peddy/tests/test.fam2.ped")))
v = p.relatedness_coefficient('101806-101806', '101811-101811')
assert v == 0.25, v
v = p.relatedness_coefficient('101806-101806', '101809-101809')
assert v == 0.25, v
# parent-child
v = p.relatedness_coefficient('101806-101806', '101653-101653')
assert v == 0.5, v