class TestTrioGenotypesPy(unittest.TestCase):
""" test the Inheritance class
"""
def setUp(self):
""" define a family and variant, and start the Inheritance class
"""
# generate a test family
child_gender = "F"
mom_aff = "1"
dad_aff = "1"
self.trio = self.create_family(child_gender, mom_aff, dad_aff)
# generate a test variant
child_var = self.create_snv(child_gender, "0/1")
mom_var = self.create_snv("F", "0/0")
dad_var = self.create_snv("M", "0/0")
self.var = TrioGenotypes(child_var)
self.var.add_mother_variant(mom_var)
self.var.add_father_variant(dad_var)
def create_snv(self, gender, genotype):
""" create a default variant
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "G"
filt = "PASS"
# set up a SNV object, since SNV inherits VcfInfo
var = SNV(chrom, pos, snp_id, ref, alt, filt)
info = "HGNC=TEST;CQ=missense_variant;DENOVO-SNP;PP_DNM=0.99"
keys = "GT:DP:TEAM29_FILTER:PP_DNM"
values = genotype + ":50:PASS:0.99"
var.add_info(info)
var.add_format(keys, values)
var.set_gender(gender)
var.set_genotype()
return var
def create_family(self, child_gender, mom_aff, dad_aff):
""" create a default family, with optional gender and parental statuses
"""
fam = Family("test")
fam.add_child("child", "child_vcf", "2", child_gender)
fam.add_mother("mother", "mother_vcf", mom_aff, "2")
fam.add_father("father", "father_vcf", dad_aff, "1")
fam.set_child()
return fam
def test_passes_de_novo_checks(self):
""" test that passes_de_novo_checks() works correctly
"""
# check that a default de novo variant passes
self.assertTrue(self.var.passes_de_novo_checks(pp_filter=0.9))
# check that vars fail without DENOVO-SNP or DENOVO-INDEL flags
del self.var.child.info["DENOVO-SNP"]
self.assertFalse(self.var.passes_de_novo_checks(pp_filter=0.9))
# make sure that DENOVO-INDEL flag can pass the de novo filter
self.var.child.info["DENOVO-INDEL"] = True
self.assertTrue(self.var.passes_de_novo_checks(pp_filter=0.9))
# check that de novos with low PP_DNM scores fail the de novo filter
self.var.child.format["PP_DNM"] = 0.0099
self.assertFalse(self.var.passes_de_novo_checks(pp_filter=0.9))
# check that de novos with low PP_DNM scores pass the de novo filter, if
# we are using a low PP_DNM threshold
self.var.child.format["PP_DNM"] = 0.0099
self.assertTrue(self.var.passes_de_novo_checks(pp_filter=0.0))
# check that we don't fail a de novo if it lacks the PP_DNM annotation
del self.var.child.format["PP_DNM"]
self.assertTrue(self.var.passes_de_novo_checks(pp_filter=0.9))
def test_passes_de_novo_checks_X_chrom(self):
""" test that passes_de_novo_checks() works on the X chromosome
"""
# check that a male X chrom de novo passes
self.trio.child.gender = "M"
self.var.inheritance_type = "XChrMale"
self.var.child.format["GT"] = "1/1"
self.var.child.set_genotype()
self.assertTrue(self.var.passes_de_novo_checks(pp_filter=0.9))
# and change a field so that it would fail
del self.var.child.info["DENOVO-SNP"]
self.assertFalse(self.var.passes_de_novo_checks(pp_filter=0.9))
# and change the variant fom a male X de novo genotype
self.var.child.format["GT"] = "1/0"
self.var.child.set_genotype()
self.assertTrue(self.var.passes_de_novo_checks(pp_filter=0.9))
# now check that a female X chrom de novo passes
self.trio.child.gender = "F"
self.var.inheritance_type = "XChrFemale"
self.var.child.set_genotype()
self.var.child.info["DENOVO-SNP"] = True
self.assertTrue(self.var.passes_de_novo_checks(pp_filter=0.9))
def test_get_de_novo_genotype(self):
""" check that get_de_novo_genotype() works correctly
"""
self.var.inheritance_type = "autosomal"
self.assertEqual(self.var.get_de_novo_genotype(), (1, 0, 0))
self.var.inheritance_type = "XChrFemale"
self.assertEqual(self.var.get_de_novo_genotype(), (1, 0, 0))
# we double the alt count for males on the X, so a de novo genotype
# differes from the other situations
self.var.inheritance_type = "XChrMale"
self.assertEqual(self.var.get_de_novo_genotype(), (2, 0, 0))
def test_get_trio_genotype(self):
""" test that get_trio_genotype() works correctly
"""
# check that the defaul var gives the expected genotypes
self.assertEqual(self.var.get_trio_genotype(), (1, 0, 0))
# check that different genotypes still work
self.var.mother.format["GT"] = "1/1"
self.var.mother.set_genotype()
self.assertEqual(self.var.get_trio_genotype(), (1, 2, 0))
# check that probands only give NA genotypes for parents
del self.var.mother
del self.var.father
self.assertEqual(self.var.get_trio_genotype(), (1, "NA", "NA"))
def test_convert_chrom_to_int(self):
""" test that convert_chrom_to_int() works correctly
"""
# check that an autosomal chrom works
self.assertEqual(self.var.convert_chrom_to_int("1"), 1)
# check that an X chrom works
self.assertEqual(self.var.convert_chrom_to_int("X"), 23)
# check that an X chrom works
self.assertEqual(self.var.convert_chrom_to_int("chrX"), 23)
# check that a Y chrom works
self.assertEqual(self.var.convert_chrom_to_int("chrY"), 24)
