class TestInheritancePy(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 list of variants
self.variants = [self.create_variant(child_gender)]
self.variants.append(self.create_variant(child_gender))
# make sure we've got known genes data
self.known_genes = {
"TEST": {
"inh": ["Monoallelic"],
"confirmed_status": ["Confirmed DD Gene"]
}
}
self.inh = Autosomal(self.variants, self.trio, self.known_genes,
"TEST")
def create_snv(self, gender, genotype, chrom, pos, cq=None):
""" create a default variant
"""
snp_id = "."
ref = "A"
alt = "G"
filt = "PASS"
if cq is None:
cq = "missense_variant"
# set up a SNV object, since SNV inherits VcfInfo
var = SNV(chrom, pos, snp_id, ref, alt, filt)
info = "HGNC=TEST;CQ={};random_tag".format(cq)
format_keys = "GT:DP"
sample_values = genotype + ":50"
var.add_info(info)
var.add_format(format_keys, sample_values)
var.set_gender(gender)
var.set_genotype()
return var
def create_cnv(self, gender, inh, chrom, pos, cq=None):
""" create a default variant
"""
snp_id = "."
ref = "A"
alt = "<DEL>"
filt = "PASS"
if cq is None:
cq = "transcript_ablation"
# set up a SNV object, since SNV inherits VcfInfo
var = CNV(chrom, pos, snp_id, ref, alt, filt)
info = "CQ={};HGNC=TEST;HGNC_ALL=TEST;END=16000000;SVLEN=5000".format(
cq)
format_keys = "INHERITANCE:DP"
sample_values = inh + ":50"
var.add_info(info)
var.add_format(format_keys, sample_values)
var.set_gender(gender)
var.set_genotype()
return var
def create_variant(self,
child_gender,
chrom="1",
position="15000000",
cq=None):
""" creates a TrioGenotypes variant
"""
# generate a test variant
try:
child_var = self.create_snv(child_gender, "0/1", chrom, position,
cq)
except ValueError:
child_var = self.create_snv(child_gender, "1/1", chrom, position,
cq)
mom_var = self.create_snv("F", "0/0", chrom, position, cq)
dad_var = self.create_snv("M", "0/0", chrom, position, cq)
var = TrioGenotypes(child_var)
var.add_mother_variant(mom_var)
var.add_father_variant(dad_var)
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_check_inheritance_mode_matches_gene_mode(self):
""" test that check_inheritance_mode_matches_gene_mode() works correctly
"""
# check that the default inheritance types have been set up correctly
self.assertEqual(self.inh.inheritance_modes,
{"Monoallelic", "Biallelic", "Both"})
# make sure that the default var and gene inheritance work
self.assertTrue(self.inh.check_inheritance_mode_matches_gene_mode())
# check that no gene inheritance overlap fails
self.inh.gene_inheritance = {"Mosaic"}
self.inh.inheritance_modes = {"Monoallelic", "Biallelic", "Both"}
self.assertFalse(self.inh.check_inheritance_mode_matches_gene_mode())
# check that a single inheritance type still works
self.inh.gene_inheritance = {"Monoallelic"}
self.assertTrue(self.inh.check_inheritance_mode_matches_gene_mode())
# check that multiple inheritance types for a gene still work
self.inh.gene_inheritance = {"Monoallelic", "Biallelic"}
self.assertTrue(self.inh.check_inheritance_mode_matches_gene_mode())
# check that extra inheritance modes are included still work
self.inh.gene_inheritance = {"Monoallelic", "Biallelic", "Mosaic"}
self.assertTrue(self.inh.check_inheritance_mode_matches_gene_mode())
def test_set_trio_genotypes(self):
""" test that set_trio_genotypes() works correctly
"""
# set the genotypes using the default variant
var = self.variants[0]
self.inh.set_trio_genotypes(var)
# the genotypes for the inh object should match the vars genotypes
self.assertEqual(self.inh.child, var.child)
self.assertEqual(self.inh.mom, var.mother)
self.assertEqual(self.inh.dad, var.father)
# now remove the parents before re-setting the genotypes
del var.mother
del var.father
self.inh.trio.father = None
self.inh.trio.mother = None
self.inh.set_trio_genotypes(var)
# the child should match the vars genotypes, but the parent's
# genotypes should be None
self.assertEqual(self.inh.child, var.child)
self.assertIsNone(self.inh.mom)
self.assertIsNone(self.inh.dad)
def test_add_variant_to_appropriate_list(self):
""" test that add_variant_to_appropriate_list() works correctly
"""
var = self.variants[0]
inheritance = "Monoallelic"
check = "compound_het"
# check that compound_het vars are only added to the compound_het list
self.inh.compound_hets = []
self.inh.candidates = []
self.inh.add_variant_to_appropriate_list(var, check, inheritance)
self.assertEqual(self.inh.candidates, [])
self.assertEqual(self.inh.compound_hets,
[(var, (check, ), (inheritance, ))])
# check that single_variant vars are only added to the candidates list
self.inh.compound_hets = []
self.inh.candidates = []
check = "single_variant"
self.inh.add_variant_to_appropriate_list(var, check, inheritance)
self.assertEqual(self.inh.candidates, [(var, [check], [inheritance])])
self.assertEqual(self.inh.compound_hets, [])
# check that other vars aren't added either list
self.inh.compound_hets = []
self.inh.candidates = []
check = "nothing"
self.inh.add_variant_to_appropriate_list(var, check, inheritance)
self.assertEqual(self.inh.candidates, [])
self.assertEqual(self.inh.compound_hets, [])
def test_check_if_any_variant_is_cnv(self):
""" test if check_if_any_variant_is_cnv() works correctly
"""
# generate a test variant
chrom = "1"
position = "60000"
child_var = self.create_cnv("F", "unknown", chrom, position)
mom_var = self.create_cnv("F", "unknown", chrom, position)
dad_var = self.create_cnv("M", "unknown", chrom, position)
cnv_var = TrioGenotypes(child_var)
cnv_var.add_mother_variant(mom_var)
cnv_var.add_father_variant(dad_var)
# check that all variants=SNV returns False
self.assertFalse(self.inh.check_if_any_variant_is_cnv())
# add a CNV to the variants, then check that we find a CNV
self.inh.variants.append(cnv_var)
self.assertTrue(self.inh.check_if_any_variant_is_cnv())
def set_compound_het_var(self, var, geno):
""" convenience function to set the trio genotypes for a variant
"""
genos = {"0": "0/0", "1": "0/1", "2": "1/1"}
# convert the geno codes to allele codes
child = genos[geno[0]]
mom = genos[geno[1]]
dad = genos[geno[2]]
# set the genotype field for each individual
var.child.format["GT"] = child
var.mother.format["GT"] = mom
var.father.format["GT"] = dad
# and set th genotype for each individual
var.child.set_genotype()
var.mother.set_genotype()
var.father.set_genotype()
# set the trio genotypes for the inheritance object
return var
def test_check_compound_hets(self):
""" test that check_compound_hets() works correctly for autosomal vars
"""
# set some variants, so we can alter them later
var1 = self.create_variant("F",
chrom="1",
position="15000000",
cq="stop_gained")
var2 = self.create_variant("F",
chrom="1",
position="16000000",
cq="stop_gained")
var3 = self.create_variant("F",
chrom="1",
position="17000000",
cq="stop_gained")
# set the inheritance type, the compound het type ("compound_het"
# for autosomal variants, and start autosomal inheritance)
# known_genes = "Biallelic"
known_genes = {
"TEST": {
"inh": ["Biallelic"],
"confirmed_status": ["Confirmed DD Gene"]
}
}
self.inh = Autosomal([var1, var2, var3], self.trio, known_genes,
"TEST")
variants = [(), ()]
# check the expected "110, 101" combo passes
variants[0] = (self.set_compound_het_var(var1, "110"), )
variants[1] = (self.set_compound_het_var(var2, "101"), )
self.assertEqual(sorted(self.inh.check_compound_hets(variants)),
sorted(variants))
# check that > 2 valid compound hets passes all variants
variants = [(), (), ()]
variants[0] = (self.set_compound_het_var(var1, "110"), )
variants[1] = (self.set_compound_het_var(var2, "101"), )
variants[2] = (self.set_compound_het_var(var3, "110"), )
self.assertEqual(sorted(self.inh.check_compound_hets(variants)),
sorted(variants))
# check that a single var fails to give compound hets
single_var = variants[:1]
self.assertEqual(self.inh.check_compound_hets(single_var), [])
# check that zero length list gives no compound hets
no_vars = []
self.assertEqual(self.inh.check_compound_hets(no_vars), [])
def test_is_compound_pair_identical_variants(self):
""" check that is_compound_pair() excludes compound pairs where the
members are identical
"""
# set some variants, so we can alter them later
var1 = self.create_variant("F",
chrom="1",
position="150",
cq="stop_gained")
var2 = self.create_variant("F",
chrom="1",
position="160",
cq="stop_gained")
var1 = self.set_compound_het_var(var1, "110")
var2 = self.set_compound_het_var(var2, "101")
# don't include pairs where the first and the second variant are identical
self.assertFalse(self.inh.is_compound_pair(var1, var1))
# make sure it works normally
self.assertTrue(self.inh.is_compound_pair(var1, var2))
def test_is_compound_pair_both_missense_with_parents(self):
"""check that is_compound_pair() excludes pairs where both are missense
"""
# set some variants, so we can alter them later
var1 = self.create_variant("F",
chrom="1",
position="150",
cq="missense_variant")
var2 = self.create_variant("F",
chrom="1",
position="160",
cq="missense_variant")
var3 = self.create_variant("F",
chrom="1",
position="160",
cq="inframe_deletion")
var4 = self.create_variant("F",
chrom="1",
position="160",
cq="stop_gained")
var1 = self.set_compound_het_var(var1, "110")
var2 = self.set_compound_het_var(var2, "101")
var3 = self.set_compound_het_var(var3, "101")
var4 = self.set_compound_het_var(var4, "101")
# dont exclude pairs where both members are not loss-of-function if the
# proband has parents
self.assertTrue(self.inh.is_compound_pair(var1, var2))
self.assertTrue(self.inh.is_compound_pair(var1, var3))
# make sure it works normally
self.assertTrue(self.inh.is_compound_pair(var1, var4))
def test_is_compound_pair_both_missense_without_parents(self):
"""check that is_compound_pair() excludes pairs where both are missense
"""
# set some variants, so we can alter them later
var1 = self.create_variant("F",
chrom="1",
position="150",
cq="missense_variant")
var2 = self.create_variant("F",
chrom="1",
position="160",
cq="missense_variant")
var3 = self.create_variant("F",
chrom="1",
position="160",
cq="inframe_deletion")
var4 = self.create_variant("F",
chrom="1",
position="160",
cq="stop_gained")
var1 = self.set_compound_het_var(var1, "110")
var2 = self.set_compound_het_var(var2, "101")
var3 = self.set_compound_het_var(var3, "101")
var4 = self.set_compound_het_var(var4, "101")
# drop the parents
self.inh.trio.father = None
self.inh.trio.mother = None
# exclude pairs where both members are not loss-of-function
self.assertFalse(self.inh.is_compound_pair(var1, var2))
self.assertFalse(self.inh.is_compound_pair(var1, var3))
# make sure it works if one variant is loss-of-function
self.assertTrue(self.inh.is_compound_pair(var1, var4))
def test_is_compound_pair_unknown_gene(self):
"""check that is_compound_pair() excludes pairs for unknown genes
"""
# set some variants, so we can alter them later
var1 = self.create_variant("F",
chrom="1",
position="150",
cq="stop_gained")
var2 = self.create_variant("F",
chrom="1",
position="160",
cq="stop_gained")
var1 = self.set_compound_het_var(var1, "110")
var2 = self.set_compound_het_var(var2, "101")
var1.child.genes = ["."]
var2.child.genes = ["."]
# exclude pairs where both members are not loss-of-function
self.assertFalse(self.inh.is_compound_pair(var1, var2))
def test_is_compound_pair_cnv(self):
""" check that is_compound_pair() includes pairs with CNVs
"""
# generate a test variant
chrom = "1"
position = "60000"
child_var = self.create_cnv("F", "unknown", chrom, position)
mom_var = self.create_cnv("F", "unknown", chrom, position)
dad_var = self.create_cnv("M", "unknown", chrom, position)
cnv = TrioGenotypes(child_var)
cnv.add_mother_variant(mom_var)
cnv.add_father_variant(dad_var)
# set some variants, so we can alter them later
snv = self.create_variant("F",
chrom="1",
position="150",
cq="stop_gained")
snv = self.set_compound_het_var(snv, "110")
# exclude pairs where both members are not loss-of-function
self.assertTrue(self.inh.is_compound_pair(cnv, snv))
def test_is_compound_pair_proband_only(self):
""" check that is_compound_pair() includes proband-only pairs
"""
fam = Family("test")
fam.add_child("child", "child_vcf", "2", "F")
fam.set_child()
# set some variants, so we can alter them later
var1 = self.create_variant("F",
chrom="1",
position="150",
cq="stop_gained")
var2 = self.create_variant("F",
chrom="1",
position="160",
cq="stop_gained")
inh = Autosomal([var1, var2], fam, self.known_genes, "TEST")
# check that a proband-only passes, regardless of the parental genotypes
self.assertTrue(inh.is_compound_pair(var1, var2))
def test_is_compound_pair_allosomal(self):
""" check that is_compound_pair() works when the father is affected
"""
# set some variants, so we can alter them later
var1 = self.create_variant("M",
chrom="X",
position="150",
cq="stop_gained")
var2 = self.create_variant("M",
chrom="X",
position="160",
cq="stop_gained")
var1 = self.set_compound_het_var(var1, "210")
var2 = self.set_compound_het_var(var2, "202")
# check when the father is unaffected
self.assertFalse(self.inh.is_compound_pair(var1, var2))
# now check when the father is affected
self.inh.father_affected = True
self.assertTrue(self.inh.is_compound_pair(var1, var2))
# make sure we can't set the father as het on the X chrom
with self.assertRaises(ValueError):
self.set_compound_het_var(var2, "201")
def test_is_compound_pair_genotype_combinations(self):
""" check the various genotype combinations for a compound het
"""
# set some variants, so we can alter them later
var1 = self.create_variant("M",
chrom="1",
position="150",
cq="stop_gained")
var2 = self.create_variant("M",
chrom="1",
position="160",
cq="stop_gained")
var1 = self.set_compound_het_var(var1, "110")
var2 = self.set_compound_het_var(var2, "101")
# check that the expected scenario passes
self.assertTrue(self.inh.is_compound_pair(var1, var2))
# check that compound hets with de novos fail
var1 = self.set_compound_het_var(var1, "100")
var2 = self.set_compound_het_var(var2, "101")
self.assertFalse(self.inh.is_compound_pair(var1, var2))
# check that compound hets have to be transmitted from both parents
var1 = self.set_compound_het_var(var1, "101")
var2 = self.set_compound_het_var(var2, "101")
self.assertFalse(self.inh.is_compound_pair(var1, var2))
# check that compound hets have to be transmitted from both parents
var1 = self.set_compound_het_var(var1, "110")
var2 = self.set_compound_het_var(var2, "110")
self.assertFalse(self.inh.is_compound_pair(var1, var2))
# make sure that only compound hets in trans pass. We exclude
var1 = self.set_compound_het_var(var1, "111")
var2 = self.set_compound_het_var(var2, "101")
self.assertFalse(self.inh.is_compound_pair(var1, var2))
var1 = self.set_compound_het_var(var1, "111")
var2 = self.set_compound_het_var(var2, "111")
self.assertFalse(self.inh.is_compound_pair(var1, var2))
