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 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_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_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_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()
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
1 mom grandpa grandma 2 2
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
