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_warnings():
with redirect_err() as out:
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
mom = Sample('fam1', 'mom', '-9', '-9', '1', '2')
dad = Sample('fam1', 'dad', '-9', '-9', '2', '2')
kid.mom = mom
kid.dad = dad
v = out.getvalue()
assert "'dad' is dad but has female sex" in v, v
assert "'mom' is mom but has male sex" in v, v
with redirect_err() as out:
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
mom = Sample('fam1', 'mom', '-9', '-9', '-9', '2')
kid.mom = mom
v = out.getvalue()
assert "'mom' is mom but has unknown sex. Setting to female" in v
with redirect_err() as out:
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
dad = Sample('fam1', 'dad', '-9', '-9', '-9', '2')
kid.dad = dad
v = out.getvalue()
assert "'dad' is dad but has unknown sex. Setting to male" in v
with redirect_err() as out:
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
kid.dad = kid
v = out.getvalue()
assert "'kid' is dad of self" in v, v
def test_warnings():
with redirect_err() as out:
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
mom = Sample('fam1', 'mom', '-9', '-9', '1', '2')
dad = Sample('fam1', 'dad', '-9', '-9', '2', '2')
kid.mom = mom
kid.dad = dad
v = out.getvalue()
assert "'dad' is dad but has female sex" in v, v
assert "'mom' is mom but has male sex" in v, v
with redirect_err() as out:
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
mom = Sample('fam1', 'mom', '-9', '-9', '-9', '2')
kid.mom = mom
v = out.getvalue()
assert "'mom' is mom but has unknown sex. Setting to female" in v
with redirect_err() as out:
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
dad = Sample('fam1', 'dad', '-9', '-9', '-9', '2')
kid.dad = dad
v = out.getvalue()
assert "'dad' is dad but has unknown sex. Setting to male" in v
with redirect_err() as out:
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
kid.dad = kid
v = out.getvalue()
assert "'kid' is dad of self" in v, v
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_relation():
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
dad = Sample('fam1', 'dad', '-9', '-9', '1', '2')
mom = Sample('fam1', 'mom', '-9', '-9', '2', '2')
kid.mom = mom
kid.dad = dad
from io import StringIO
p = Ped(StringIO())
p.families['fam1'] = Family([kid, mom, dad])
assert p.relation("mom", "dad") == "mom-dad"
def test_relation():
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
dad = Sample('fam1', 'dad', '-9', '-9', '1', '2')
mom = Sample('fam1', 'mom', '-9', '-9', '2', '2')
kid.mom = mom
kid.dad = dad
from io import StringIO
p = Ped(StringIO())
p.families['fam1'] = Family([kid, mom, dad])
assert p.relation("mom", "dad") == "mom-dad"
