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 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_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_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_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']
from __future__ import print_function
import sys
from inheritance import Sample, Family, EvalFamily
mom = Sample('mom', affected=False)
dad = Sample('dad', affected=False)
kid = Sample('kid', affected=True)
kid.mom, kid.dad = mom, dad
fam = Family([mom, dad, kid], 'a')
def make_fam1():
# only 1 affected kid.
fam = Family.from_ped("""\
#family_id sample_id paternal_id maternal_id sex phenotype
1 dad 0 0 1 1
1 mom grandpa grandma 2 1
1 kid dad mom 1 2
1 kid2 dad mom 1 1
1 grandma 0 0 2 1
1 grandpa 0 0 1 1""")
return fam
def make_fam2():
# 1 affected kid, parent, grandparent
fam = Family.from_ped("""\
#family_id sample_id paternal_id maternal_id sex phenotype
1 dad 0 0 1 1
