def test_comp_het_one_parent():
mom._i = 0
kid._i = 1
kid.dad = None
kid.mom = None
efam = EvalFamily(Family([mom, kid], 'pair_mom'))
efam.gt_types = [Family.HET] * 2
res = efam.comp_het_pair([Family.HET] * 2, ["A/C"] * 2,
[Family.HET] * 2, ["A/C"] * 2,
[False] * 2, [False] * 2,
"A", "C", "A", "C")
assert res['candidate']
assert res['priority'] == 3, res['priority']
res = efam.comp_het_pair([Family.HOM_REF, Family.HET] * 2, ["A/A", "A/C"],
[Family.HET, Family.HET], ["A/C"] * 2,
[False] * 2, [False] * 2,
"A", "C", "A", "C")
assert res['candidate']
assert res['priority'] == 2, res['priority']
res = efam.comp_het_pair([Family.HOM_REF, Family.HOM_REF] * 2, ["A/A", "A/A"],
[Family.HET, Family.HET], ["A/C"] * 2,
[False] * 2, [False] * 2,
"A", "C", "A", "C")
assert not res['candidate']
def test_comp_het_one_parent_2kids():
"""
test that we cant have a candidate when a parent is HOM_REF at both sites.
"""
mom._i = 0
kid._i = 1
kid2._i = 2
kid.dad = None
kid.mom = None
kid.mom = mom
efam = EvalFamily(Family([mom, kid, kid2], '2kids'))
efam.gt_types = [Family.HOM_REF, Family.HET, Family.HET]
res = efam.comp_het_pair([Family.HOM_REF, Family.HET, Family.HET],
["T/T", "T/C", "T/C"],
[Family.HOM_REF, Family.HET, Family.HET],
["A/A", "A/C", "A/C"], [False] * 3, [False] * 3,
"T",
"C",
"A",
"C",
fast_mode=False,
allow_unaffected=True)
assert not res['candidate'], res
def test_comphet_pattern():
fam = make_fam2()
efam = EvalFamily(fam)
assert [f.affected for f in efam.subjects] == [False, True, True, False, True, False]
gt_types1 = [Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET, Family.HOM_REF]
gt_types2 = [Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET, Family.HOM_REF]
efam.gt_types = gt_types1
gt_bases1 = ["A/C", "A/A", "A/C", "A/A", "A/A", "A/C", "A/A"]
gt_bases2 = ["A/C", "A/A", "A/C", "A/A", "A/A", "A/C", "A/A"]
res = efam.comp_het_pair(gt_types1, gt_bases1, gt_types2, gt_bases2)
def test_comp_het_singleton():
kid = Sample('kid', affected=True)
efam = EvalFamily(Family([kid], 'singleton'))
efam.gt_types = [Family.HET]
res = efam.comp_het_pair([Family.HET], ["A/C"], [Family.HET], ["A/C"],
[False], [False], "A", "C", "A", "C")
assert res['candidate']
assert res['priority'] == 2, res
def test_comp_het_singleton():
kid = Sample('kid', affected=True)
efam = EvalFamily(Family([kid], 'singleton'))
efam.gt_types = [Family.HET]
res = efam.comp_het_pair([Family.HET], ["A/C"], [Family.HET], ["A/C"],
[False], [False], "A", "C", "A", "C")
assert res['candidate']
assert res['priority'] == 2, res
def test_comp_het_all_hets():
efam = EvalFamily(Family([dad, mom, kid], 'triox'))
efam.gt_types = [Family.HET] * 3
res = efam.comp_het_pair([Family.HET] * 3, ["A/C"] * 3,
[Family.HET] * 3, ["A/C"] * 3,
[False] * 3, [False] * 3, "A", "C", "A", "C")
assert res['candidate']
assert res['priority'] == 3
def test_comp_het_all_hets():
efam = EvalFamily(Family([dad, mom, kid], 'triox'))
efam.gt_types = [Family.HET] * 3
res = efam.comp_het_pair([Family.HET] * 3, ["A/C"] * 3, [Family.HET] * 3,
["A/C"] * 3, [False] * 3, [False] * 3, "A", "C",
"A", "C")
assert res['candidate']
assert res['priority'] == 3
def test_comp_het_missing():
fam = make_fam1()
efam = EvalFamily(fam)
assert [f.affected for f in efam.subjects] == [False, False, True, False, False, False]
gt_types1 = [Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET, Family.HOM_REF]
gt_types2 = [Family.HET, Family.HOM_REF, Family.HET, Family.HOM_REF, Family.HOM_REF, Family.HOM_REF]
gt_bases1 = ["A/A", "A/C", ".", "A/A", "A/A", "A/C", "A/A"]
gt_bases2 = ["A/C", "A/A", "A/C", "A/A", "A/A", "A/A", "A/A"]
gt_phases = [False] * len(gt_bases2)
efam.gt_types = gt_types1
res = efam.comp_het_pair(gt_types1, gt_bases1, gt_types2, gt_bases2,
gt_phases, gt_phases, "A", "C", "A", "C")
assert res['candidate'] is False, res
def test_comp_het_one_parent():
mom._i = 0
kid._i = 1
kid.dad = None
kid.mom = None
efam = EvalFamily(Family([mom, kid], 'pair_mom'))
efam.gt_types = [Family.HET] * 2
res = efam.comp_het_pair([Family.HET] * 2, ["A/C"] * 2, [Family.HET] * 2,
["A/C"] * 2, [False] * 2, [False] * 2, "A", "C",
"A", "C")
assert res['candidate']
assert res['priority'] == 3, res['priority']
res = efam.comp_het_pair([Family.HOM_REF, Family.HET] * 2, ["A/A", "A/C"],
[Family.HET, Family.HET], ["A/C"] * 2,
[False] * 2, [False] * 2, "A", "C", "A", "C")
assert res['candidate']
assert res['priority'] == 2, res['priority']
res = efam.comp_het_pair([Family.HOM_REF, Family.HOM_REF] * 2,
["A/A", "A/A"], [Family.HET, Family.HET],
["A/C"] * 2, [False] * 2, [False] * 2, "A", "C",
"A", "C")
assert not res['candidate']
def test_comphet_pattern():
fam = make_fam2()
efam = EvalFamily(fam)
assert [f.affected
for f in efam.subjects] == [False, True, True, False, True, False]
gt_types1 = [
Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET,
Family.HOM_REF
]
gt_types2 = [
Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET,
Family.HOM_REF
]
efam.gt_types = gt_types1
gt_bases1 = ["A/C", "A/A", "A/C", "A/A", "A/A", "A/C", "A/A"]
gt_bases2 = ["A/C", "A/A", "A/C", "A/A", "A/A", "A/C", "A/A"]
res = efam.comp_het_pair(gt_types1, gt_bases1, gt_types2, gt_bases2)
def test_comp_het_missing():
fam = make_fam1()
efam = EvalFamily(fam)
assert [f.affected for f in efam.subjects
] == [False, False, True, False, False, False]
gt_types1 = [
Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET,
Family.HOM_REF
]
gt_types2 = [
Family.HET, Family.HOM_REF, Family.HET, Family.HOM_REF, Family.HOM_REF,
Family.HOM_REF
]
gt_bases1 = ["A/A", "A/C", ".", "A/A", "A/A", "A/C", "A/A"]
gt_bases2 = ["A/C", "A/A", "A/C", "A/A", "A/A", "A/A", "A/A"]
gt_phases = [False] * len(gt_bases2)
efam.gt_types = gt_types1
res = efam.comp_het_pair(gt_types1, gt_bases1, gt_types2, gt_bases2,
gt_phases, gt_phases, "A", "C", "A", "C")
assert res['candidate'] is False, res
def test_comp_het_one_parent_2kids():
"""
test that we cant have a candidate when a parent is HOM_REF at both sites.
"""
mom._i = 0
kid._i = 1
kid2._i = 2
kid.dad = None
kid.mom = None
kid.mom = mom
efam = EvalFamily(Family([mom, kid, kid2], '2kids'))
efam.gt_types = [Family.HOM_REF, Family.HET, Family.HET]
res = efam.comp_het_pair(
[Family.HOM_REF, Family.HET, Family.HET],
["T/T", "T/C", "T/C"],
[Family.HOM_REF, Family.HET, Family.HET],
["A/A", "A/C", "A/C"],
[False] * 3,
[False] * 3,
"T", "C", "A", "C", fast_mode=False, allow_unaffected=True)
assert not res['candidate'], res
