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
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
