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