def test_auto_rec():
assert "gt_types[kid] == 3" in fam.auto_rec()
efam = EvalFamily(fam)
efam.gt_types = [Family.HET, Family.HET, Family.HOM_ALT]
assert efam.auto_rec()
efam.gt_types = [Family.HET, Family.HET, Family.HET]
assert not efam.auto_rec()
def test_auto_rec():
assert "gt_types[kid] == 3" in fam.auto_rec()
efam = EvalFamily(fam)
efam.gt_types = [Family.HET, Family.HET, Family.HOM_ALT]
assert efam.auto_rec()
efam.gt_types = [Family.HET, Family.HET, Family.HET]
assert not efam.auto_rec()
def test_auto_rec_extended():
fam = make_fam1()
efam = EvalFamily(fam)
efam.gt_types = [
Family.HET, Family.HET, Family.HOM_ALT, Family.HET, Family.HET,
Family.HET
]
assert efam.auto_rec()
#if grandpa is affected it is no longer autosomal recessive
efam.subjects[5].affected = True
assert not efam.auto_rec()
efam.subjects[5].affected = False
# set both kids to hom_alt:
efam.gt_types[3] = Family.HOM_ALT
assert not efam.auto_rec()
assert efam.auto_rec(only_affected=False)
# set unaffected kid back:
efam.gt_types[3] = Family.HET
# expected that is is auto_rec
assert efam.auto_rec()
# but it's not if we set all depths to 9 and have min_depth of 10
efam.gt_depths = [9] * 6
assert not efam.auto_rec(min_depth=10)
efam.gt_depths[2] = 1000
# even if affected has high depth
assert not efam.auto_rec(min_depth=10)
# passes if we meet the minimum depth
efam.gt_depths = [100] * 6
assert efam.auto_rec(min_depth=10)
# check if we have no affecteds:
efam.subjects[2].affected = False
assert not efam.auto_rec(min_depth=10)
def test_auto_rec_extended():
fam = make_fam1()
efam = EvalFamily(fam)
efam.gt_types = [Family.HET, Family.HET, Family.HOM_ALT, Family.HET, Family.HET, Family.HET]
assert efam.auto_rec()
#if grandpa is affected it is no longer autosomal recessive
efam.subjects[5].affected = True
assert not efam.auto_rec()
efam.subjects[5].affected = False
# set both kids to hom_alt:
efam.gt_types[3] = Family.HOM_ALT
assert not efam.auto_rec()
assert efam.auto_rec(only_affected=False)
# set unaffected kid back:
efam.gt_types[3] = Family.HET
# expected that is is auto_rec
assert efam.auto_rec()
# but it's not if we set all depths to 9 and have min_depth of 10
efam.gt_depths = [9] * 6
assert not efam.auto_rec(min_depth=10)
efam.gt_depths[2] = 1000
# even if affected has high depth
assert not efam.auto_rec(min_depth=10)
# passes if we meet the minimum depth
efam.gt_depths = [100] * 6
assert efam.auto_rec(min_depth=10)
# check if we have no affecteds:
efam.subjects[2].affected = False
assert not efam.auto_rec(min_depth=10)
def test_auto_rec_kid_unaffected():
kid.affected = False
efam = EvalFamily(fam)
efam.gt_types = [Family.HET, Family.HET, Family.HOM_ALT]
assert not efam.auto_rec()
kid.affected = True
def test_auto_rec_kid_unaffected():
kid.affected = False
efam = EvalFamily(fam)
efam.gt_types = [Family.HET, Family.HET, Family.HOM_ALT]
assert not efam.auto_rec()
kid.affected = True
