def test_x_dom_parents():
mom = Sample('mom', affected=False, sex='female')
dad = Sample('dad', affected=False, sex='male')
kid = Sample('kid', affected=True, sex='female')
kid.mom, kid.dad = mom, dad
efam = EvalFamily(Family([dad, mom, kid], 'trio'))
efam.gt_types = [Family.HOM_REF, Family.HOM_REF, Family.HET]
# neither parent is het
assert not efam.x_dom()
# neither parent is affected
efam.gt_types = [Family.HET, Family.HOM_REF, Family.HET]
assert not efam.x_dom()
dad.affected = True
assert efam.x_dom()
# for male, only mom must be affected
kid.sex = 'male'
assert not efam.x_dom()
def test_xdom():
efam = EvalFamily(fam)
fam.subjects[0].sex = 'female'
fam.subjects[1].sex = 'male'
fam.subjects[2].sex = 'female'
efam.gt_types = [Family.HET, Family.HOM_REF, Family.HOM_ALT]
assert not efam.x_dom()
# mom must be affected.
fam.subjects[0].affected = False
assert not efam.x_dom()
efam.gt_types[2] = Family.HET
fam.subjects[0].affected = True
assert efam.x_dom()
fam.subjects[0].affected = False
fam.subjects[1].affected = True
# dad affected, but hom_ref
assert not efam.x_dom()
efam.gt_types = [Family.HOM_REF, Family.HET, Family.HOM_ALT]
assert not efam.x_dom()
fam.subjects[0].sex = 'female'
fam.subjects[1].sex = 'male'
fam.subjects[2].sex = 'female'
efam = EvalFamily(fam)
efam.gt_types = [Family.HOM_REF, Family.HOM_ALT, Family.HET]
import sys
fam.subjects[0].affected = False
fam.subjects[1].affected = True
fam.subjects[2].affected = True
assert efam.x_dom()
def test_xdom():
efam = EvalFamily(fam)
fam.subjects[0].sex = 'female'
fam.subjects[1].sex = 'male'
fam.subjects[2].sex = 'female'
efam.gt_types = [Family.HET, Family.HOM_REF, Family.HOM_ALT]
assert not efam.x_dom()
# mom must be affected.
fam.subjects[0].affected = False
assert not efam.x_dom()
efam.gt_types[2] = Family.HET
fam.subjects[0].affected = True
assert efam.x_dom()
fam.subjects[0].affected = False
fam.subjects[1].affected = True
# dad affected, but hom_ref
assert not efam.x_dom()
efam.gt_types = [Family.HOM_REF, Family.HET, Family.HOM_ALT]
assert not efam.x_dom()
fam.subjects[0].sex = 'female'
fam.subjects[1].sex = 'male'
fam.subjects[2].sex = 'female'
efam = EvalFamily(fam)
efam.gt_types = [Family.HOM_REF, Family.HOM_ALT, Family.HET]
import sys
fam.subjects[0].affected = False
fam.subjects[1].affected = True
fam.subjects[2].affected = True
assert efam.x_dom()
def test_x_dom_parents():
mom = Sample('mom', affected=False, sex='female')
dad = Sample('dad', affected=False, sex='male')
kid = Sample('kid', affected=True, sex='female')
kid.mom, kid.dad = mom, dad
efam = EvalFamily(Family([dad, mom, kid], 'trio'))
efam.gt_types = [Family.HOM_REF, Family.HOM_REF, Family.HET]
# neither parent is het
assert not efam.x_dom()
# neither parent is affected
efam.gt_types = [Family.HET, Family.HOM_REF, Family.HET]
assert not efam.x_dom()
dad.affected = True
assert efam.x_dom()
# for male, only mom must be affected
kid.sex = 'male'
assert not efam.x_dom()
