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()
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_denovo():
fam = make_fam2()
efam = EvalFamily(fam)
assert [f.affected for f in efam.subjects] == [False, True, True, False, True, False]
efam.gt_types = [Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET, Family.HOM_REF]
assert not efam.de_novo()
def test_auto_dom_extended():
fam = make_fam2()
efam = EvalFamily(fam)
assert [f.affected for f in efam.subjects] == [False, True, True, False, True, False]
efam.gt_types = [Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET, Family.HOM_REF]
assert efam.auto_dom()
# unaffected is het:
efam.gt_types[0] = Family.HET
assert not efam.auto_dom()
assert efam.auto_dom(only_affected=False)
efam.gt_types[0] = Family.HOM_REF
assert efam.auto_dom()
efam.gt_depths = [9] * 6
assert not efam.auto_dom(min_depth=10)
# check with no unaffecteds
for f in efam.subjects:
f.affected = True
assert not efam.auto_dom()
# check with all unaffecteds
for f in efam.subjects:
f.affected = False
assert not efam.auto_dom()
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_xrec():
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 efam.x_rec()
fam.subjects[2].sex = 'male'
efam.gt_types = [Family.HET, Family.HOM_REF, Family.HOM_ALT]
assert efam.x_rec()
fam.subjects[2].sex = 'female'
# mom is hom_alt, but not affected
efam.gt_types = [Family.HOM_ALT, Family.HOM_REF, Family.HOM_ALT]
assert not efam.x_rec()
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_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_x_rec():
mom = Sample('mom_1239NIH', affected=False, sex='female')
dad = Sample('dad_1240NIH', affected=False, sex='male')
kid_aff = Sample('kidaff_1238NIH', affected=True, sex='female')
kid_aff.mom = mom
kid_aff.dad = dad
efam = EvalFamily(Family([dad, mom, kid_aff], 'oler-trio'))
# mom should be a carrier
efam.gt_types = [Family.HOM_REF, Family.HOM_REF, Family.HOM_ALT]
assert efam.x_rec()
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_x_denovo():
efam = EvalFamily(fam)
fam.subjects[0].sex = 'female'
fam.subjects[1].sex = 'male'
fam.subjects[2].sex = 'female'
efam.gt_types = [Family.HOM_REF, Family.HOM_REF, Family.HET]
assert efam.x_denovo()
efam.gt_types[1] = Family.HET
assert not efam.x_denovo()
efam.gt_types[1] = Family.HOM_REF
fam.subjects[2].sex = 'male'
assert efam.x_denovo()
def test_comphet_pair():
fam = make_fam2()
efam = EvalFamily(fam)
assert [f.affected for f in efam.subjects] == [False, True, True, False, True, False]
efam.gt_types = [Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET, Family.HOM_REF]
res = efam.comp_het()
assert res
# still ok with het
efam.gt_types[0] = Family.HET
res = efam.comp_het()
assert res
# not ok with hom_alt of unaffected
efam.gt_types[0] = Family.HOM_ALT
res = efam.comp_het()
assert not res
def test_comp_het_priority():
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/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 True, res
assert res['priority'] == 1
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_pair():
fam = make_fam2()
efam = EvalFamily(fam)
assert [f.affected
for f in efam.subjects] == [False, True, True, False, True, False]
efam.gt_types = [
Family.HOM_REF, Family.HET, Family.HET, Family.HOM_REF, Family.HET,
Family.HOM_REF
]
res = efam.comp_het()
assert res
# still ok with het
efam.gt_types[0] = Family.HET
res = efam.comp_het()
assert res
# not ok with hom_alt of unaffected
efam.gt_types[0] = Family.HOM_ALT
res = efam.comp_het()
assert not 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_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 make_fam(n_affecteds, n_unaffecteds, n_unknowns, id="xxx"):
samples = []
for i in range(n_affecteds):
samples.append(Sample('affected_%d' % i, affected=True,
sex=random.randint(1, 2), name='affected_%d' % i))
for i in range(n_unaffecteds):
samples.append(Sample('unaffected_%d' % i, affected=False,
sex=random.randint(1, 2), name='affected_%d' % i))
for i in range(n_unknowns):
samples.append(Sample('unknown_%d' % i, affected=None,
sex=random.randint(1, 2), name='affected_%d' % i))
for i in range(int((n_affecteds + n_affecteds + n_unknowns) / 2)):
sample = random.choice(samples)
if random.random() < 0.9:
try:
sample.dad = random.choice([s for s in samples if not s == sample and s.sex == 'male'])
except IndexError:
pass
if random.random() < 0.9:
try:
sample.mom = random.choice([s for s in samples if not s == sample and s.sex == 'female'])
except IndexError:
pass
fam = EvalFamily(Family(samples, 'fam_%s' % id))
fam.gt_types = [random.randrange(0, 4) for _ in range(len(samples))]
fam.gt_depths = [random.randrange(0, 100) for _ in range(len(samples))]
fam.gt_phred_ll_homref = [random.randrange(0, 100) for _ in range(len(samples))]
fam.gt_phred_ll_het = [random.randrange(0, 100) for _ in range(len(samples))]
fam.gt_phred_ll_homalt = [random.randrange(0, 100) for _ in range(len(samples))]
fam.gt_quals = [random.randrange(5, 100) for _ in range(len(samples))]
return fam
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