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_sample_str_and_from_row():
s = Sample('fam1', 'sample1', '-9', '-9', '2', '2')
assert str(s) == "fam1 sample1 -9 -9 2 2", str(s)
s2 = Sample.from_row(str(s))
assert s2.sample_id == s.sample_id
assert s2.sex == s.sex
assert s2.family_id == s.family_id
def test_dict():
s = Sample('fam1', 'sample1', '-9', '-9', '2', '2')
d = s.dict()
assert d == {
'maternal_id': '-9',
'paternal_id': '-9',
'sex': 'female',
'family_id': 'fam1',
'phenotype': 'affected',
'sample_id': 'sample1'
}, d
s = Sample('fam1', 'sample1', 'dad', 'mom', '1', '1')
d = s.dict()
assert d == {
'maternal_id': 'mom',
'paternal_id': 'dad',
'sex': 'male',
'family_id': 'fam1',
'phenotype': 'unaffected',
'sample_id': 'sample1'
}
s = Sample('fam1', 'sample1', 'dad', 'mom', '-1', '-1')
d = s.dict()
assert d == {
'maternal_id': 'mom',
'paternal_id': 'dad',
'sex': '-9',
'family_id': 'fam1',
'phenotype': 'affected',
'sample_id': 'sample1'
}, d
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_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_attrs():
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2', ['asdf', 'hello'])
assert str(kid) == "fam1 kid dad mom 2 2 asdf hello", str(kid)
assert repr(
kid
) == "Sample('fam1', 'kid', 'dad', 'mom', 'female', 'affected', ['asdf', 'hello'])", repr(
kid)
def test_family():
kid = Sample('fam1', 'kid', 'dad', 'mom', '2', '2')
mom = Sample('fam1', 'mom', '-9', '-9', '2', '2')
dad = Sample('fam1', 'dad', '-9', '-9', '1', '2')
f = Family([kid, mom, dad])
assert mom.kids == [kid]
assert dad.kids == [kid]
assert kid.dad == dad
assert kid.mom == mom
assert list(f.affecteds) == [kid, mom, dad], list(f.affecteds)
assert list(f.unaffecteds) == []
assert list(f) == [kid, mom, dad]
def test_sample_str_and_from_row():
s = Sample('fam1', 'sample1', '-9', '-9', '2', '2')
assert str(s) == "fam1 sample1 -9 -9 2 2", str(s)
s2 = Sample.from_row(str(s))
assert s2.sample_id == s.sample_id
assert s2.sex == s.sex
assert s2.family_id == s.family_id
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_dict():
s = Sample('fam1', 'sample1', '-9', '-9', '2', '2')
d = s.dict()
assert d == {'maternal_id': '-9', 'paternal_id': '-9', 'sex': 'female',
'family_id': 'fam1', 'phenotype': 'affected', 'sample_id': 'sample1'}, d
s = Sample('fam1', 'sample1', 'dad', 'mom', '1', '1')
d = s.dict()
assert d == {'maternal_id': 'mom', 'paternal_id': 'dad', 'sex': 'male', 'family_id':
'fam1', 'phenotype': 'unaffected', 'sample_id': 'sample1'}
s = Sample('fam1', 'sample1', 'dad', 'mom', '-1', '-1')
d = s.dict()
assert d == {'maternal_id': 'mom', 'paternal_id': 'dad', 'sex': '-9',
'family_id': 'fam1', 'phenotype': 'affected', 'sample_id':
'sample1'}, d
def test_sample():
s = Sample('fam1', 'sample1', '-9', '-9', '2', '2')
assert s.sex == SEX.FEMALE, (s.sex)
assert s.affected == PHENOTYPE.AFFECTED
assert s.kids == []
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():
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_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
