def test_is_compound_pair_cnv_maternal(self):
""" check that is_compound_pair() includes pairs with CNVs
"""
# generate a test variant
chrom = "1"
position = "60000"
extra = [('CIFER_INHERITANCE', 'maternal')]
child = create_cnv("F",
"maternal",
chrom=chrom,
pos=position,
format=extra)
mom = create_cnv("F", "unknown", chrom=chrom, pos=position)
dad = create_cnv("M", "unknown", chrom=chrom, pos=position)
cnv = TrioGenotypes(chrom, position, child, mom, dad)
# set some variants, so we can alter them later
snv = self.create_variant(chrom="1",
position="150",
sex="F",
cq="stop_gained")
snv = self.set_compound_het_var(snv, "101")
# check that these variants are compound hets, no matter which order
# they are given as.
self.assertTrue(self.inh.is_compound_pair(cnv, snv))
# check that if the SNV is inherited from the same parent as the CNV,
# then the pair isn't a compound het.
snv = self.set_compound_het_var(snv, "110")
self.assertFalse(self.inh.is_compound_pair(cnv, snv))
def test_is_compound_pair_cnv_maternal(self):
""" check that is_compound_pair() includes pairs with CNVs
"""
# generate a test variant
chrom = "1"
position = "60000"
extra = [('CIFER_INHERITANCE', 'maternal')]
child = create_cnv("F", "maternal", chrom=chrom, pos=position, format=extra)
mom = create_cnv("F", "unknown", chrom=chrom, pos=position)
dad = create_cnv("M", "unknown", chrom=chrom, pos=position)
cnv = TrioGenotypes(chrom, position, child, mom, dad)
# set some variants, so we can alter them later
snv = self.create_variant(chrom="1", position="150", sex="F", cq="stop_gained")
snv = self.set_compound_het_var(snv, "101")
# check that these variants are compound hets, no matter which order
# they are given as.
self.assertTrue(self.inh.is_compound_pair(cnv, snv))
# check that if the SNV is inherited from the same parent as the CNV,
# then the pair isn't a compound het.
snv = self.set_compound_het_var(snv, "110")
self.assertFalse(self.inh.is_compound_pair(cnv, snv))
def test_is_compound_pair_cnv_de_novo(self):
""" check that is_compound_pair() includes pairs with CNVs
"""
chrom = "1"
position = "60000"
extra = [('CIFER_INHERITANCE', 'not_inherited')]
child = create_cnv("F",
"maternal",
chrom=chrom,
pos=position,
format=extra)
mom = create_cnv("F", "unknown", chrom=chrom, pos=position)
dad = create_cnv("M", "unknown", chrom=chrom, pos=position)
cnv = TrioGenotypes(chrom, position, child, mom, dad)
# set some variants, so we can alter them later
snv = self.create_variant(chrom="1",
position="150",
sex="F",
cq="stop_gained")
snv = self.set_compound_het_var(snv, "101")
snv.child.format.pop("PP_DNM")
# check that these variants are compound hets, no matter which order
# they are given as.
self.assertTrue(self.inh.is_compound_pair(cnv, snv))
self.assertTrue(self.inh.is_compound_pair(snv, cnv))
#check the snv can also be maternal
snv = self.set_compound_het_var(snv, "110")
snv.child.format.pop("PP_DNM")
self.assertTrue(self.inh.is_compound_pair(snv, cnv))
def test_check_homozygous_with_cnv(self):
""" test that check_homozygous() works correctly for variant lists with CNVs
"""
# generate a test variant
chrom = "1"
position = "60000"
child = create_cnv("F", "unknown", chrom=chrom, pos=position)
mom = create_cnv("F", "unknown", chrom=chrom, pos=position)
dad = create_cnv("M", "unknown", chrom=chrom, pos=position)
cnv = TrioGenotypes(chrom, position, child, mom, dad)
var = self.variants[0]
# check for trio = 200, which is non-mendelian
self.set_trio_genos(var, "200")
self.assertEqual(self.inh.check_homozygous("Biallelic"), "nothing")
self.assertEqual(self.inh.log_string, "non-mendelian trio")
# check when a CNV is in the variants list
self.inh.variants.append(cnv)
self.assertEqual(self.inh.check_homozygous("Biallelic"),
"compound_het")
self.assertEqual(self.inh.log_string,
"non-mendelian, but CNV might affect call")
def create_variant(self, sex):
""" creates a TrioGenotypes variant
"""
chrom = '1'
position = '150'
info = 'CNS=3;CALLSOURCE=aCGH'
format = [('CIFER_INHERITANCE', 'uncertain')]
# generate a test variant
child = create_cnv(sex, "unknown", extra_info=info, format=format)
mom = create_cnv("F", "unknown", extra_info=info, format=format)
dad = create_cnv("M", "unknown", extra_info=info, format=format)
return TrioGenotypes(chrom, position, child, mom, dad)
def create_variant(self, sex):
""" creates a TrioGenotypes variant
"""
chrom = '1'
position = '150'
info = 'CNS=3;CALLSOURCE=aCGH'
format = [('CIFER_INHERITANCE', 'uncertain')]
# generate a test variant
child = create_cnv(sex, "unknown", extra_info=info, format=format)
mom = create_cnv("F", "unknown", extra_info=info, format=format)
dad = create_cnv("M", "unknown", extra_info=info, format=format)
return TrioGenotypes(chrom, position, child, mom, dad)
def setUp(self):
""" define a default VcfInfo object
"""
extra = "HGNC=OR5A1;CQ=missense_variant;CONVEX;RC50INTERNALFREQ=0.005;COMMONFORWARDS=0.000;MEANLR2=0.5;MADL2R=0.02"
cnv = create_cnv('F', 'deNovo', extra_info=extra)
self.var = ExomeCNV(cnv)
def setUp(self):
""" define a default VcfInfo object
"""
extra = 'OR5A1;CNSOLIDATE;WSCORE=0.5;CALLP=0.000;COMMONFORWARDS=0.000;MEANLR2=0.5;MADL2R=0.02;'
cnv = create_cnv('F', 'deNovo', extra_info=extra)
self.var = ACGH_CNV(cnv)
def setUp(self):
""" define a default VcfInfo object
"""
extra = "OR5A1;CQ=missense_variant;CONVEX;RC50INTERNALFREQ=0.005;COMMONFORWARDS=0.000;MEANLR2=0.5;MADL2R=0.02"
cnv = create_cnv('F', 'deNovo', extra_info=extra)
self.var = ExomeCNV(cnv)
def setUp(self):
""" define a default VcfInfo object
"""
extra = 'OR5A1;CNSOLIDATE;WSCORE=0.5;CALLP=0.000;COMMONFORWARDS=0.000;MEANLR2=0.5;MADL2R=0.02;'
cnv = create_cnv('F', 'deNovo', extra_info=extra)
self.var = ACGH_CNV(cnv)
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 = create_cnv("F", "unknown", chrom=chrom, pos=position)
mom = create_cnv("F", "unknown", chrom=chrom, pos=position)
dad = create_cnv("M", "unknown", chrom=chrom, pos=position)
cnv_var = TrioGenotypes(chrom, position, child, mom, dad)
# 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 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 = create_cnv("F", "unknown", chrom=chrom, pos=position)
mom = create_cnv("F", "unknown", chrom=chrom, pos=position)
dad = create_cnv("M", "unknown", chrom=chrom, pos=position)
cnv_var = TrioGenotypes(chrom, position, child, mom, dad)
# 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 test_get_parental_var_cnv(self):
''' check that get_parental_var() works correctly for CNVs
'''
sex = 'F'
var = create_cnv(sex, 'deNovo')
mom = Person('fam_id', 'mom', '0', '0', 'F', '1', '/PATH')
parental_vars = []
self.assertEqual(
get_parental_var(var, parental_vars, mom),
CNV(chrom="1",
position=150,
id=".",
ref="A",
alts="<REF>",
qual='1000',
filter="PASS",
info=str(var.info),
format='INHERITANCE',
sample='uncertain',
gender="female",
mnv_code=None))
# check that even if a CNV exist in the parent at a matching site, we
# still create a new CNV objectr for the parent
mother_var = create_cnv(sex, 'uncertain')
self.assertEqual(
get_parental_var(var, [mother_var], mom),
CNV(chrom="1",
position=150,
id=".",
ref="A",
alts="<REF>",
qual='1000',
filter="PASS",
info=str(var.info),
format='INHERITANCE',
sample='uncertain',
gender="female",
mnv_code=None))
def test_get_parental_var_cnv(self):
''' check that get_parental_var() works correctly for CNVs
'''
sex = 'F'
var = create_cnv(sex, 'deNovo')
mom = Person('fam_id', 'mom', '0', '0', 'F', '1', '/PATH')
parental_vars = []
self.assertEqual(self.vcf_loader.get_parental_var(var, parental_vars,
mom), CNV(chrom="1", position=150, id=".", ref="A",
alts="<REF>", filter="PASS", info=var.get_info_as_string(),
format='INHERITANCE', sample='uncertain', gender="female",
mnv_code=None))
# check that even if a CNV exist in the parent at a matching site, we
# still create a new CNV objectr for the parent
mother_var = create_cnv(sex, 'uncertain')
self.assertEqual(self.vcf_loader.get_parental_var(var, [mother_var],
mom), CNV(chrom="1", position=150, id=".", ref="A",
alts="<REF>", filter="PASS", info=var.get_info_as_string(),
format='INHERITANCE', sample='uncertain', gender="female",
mnv_code=None))
def test_check_homozygous_with_cnv(self):
""" test that check_homozygous() works correctly for variant lists with CNVs
"""
# generate a test variant
chrom = "1"
position = "60000"
child = create_cnv("F", "unknown", chrom=chrom, pos=position)
mom = create_cnv("F", "unknown", chrom=chrom, pos=position)
dad = create_cnv("M", "unknown", chrom=chrom, pos=position)
cnv = TrioGenotypes(chrom, position, child, mom, dad)
var = self.variants[0]
# check for trio = 200, which is non-mendelian
self.set_trio_genos(var, "200")
self.assertEqual(self.inh.check_homozygous("Biallelic"), "nothing")
self.assertEqual(self.inh.log_string, "non-mendelian trio")
# check when a CNV is in the variants list
self.inh.variants.append(cnv)
self.assertEqual(self.inh.check_homozygous("Biallelic"), "compound_het")
self.assertEqual(self.inh.log_string, "non-mendelian, but CNV might affect call")
def test_get_parental_var_cnv_maternally_inherited(self):
''' test that we can construct a maternally inherited CNV
'''
sex = 'F'
mom = Person('fam_id', 'mom', '0', '0', 'F', '1', '/PATH')
# check that even if a CNV exist in the parent at a matching site, we
# still create a new CNV object for the parent
var = create_cnv(sex, 'maternal')
self.assertEqual(get_parental_var(var, [], mom),
CNV(chrom="1", position=150, id=".", ref="A",
alts="<DUP>", qual='1000',filter="PASS", info=str(var.info),
format='INHERITANCE', sample='uncertain', gender="female",
mnv_code=None))
def test_get_parental_var_cnv_maternally_inherited(self):
'''
'''
sex = 'F'
mom = Person('fam_id', 'mom', '0', '0', 'F', '1', '/PATH')
# check that even if a CNV exist in the parent at a matching site, we
# still create a new CNV object for the parent
var = create_cnv(sex, 'maternal')
self.assertEqual(self.vcf_loader.get_parental_var(var, [], mom),
CNV(chrom="1", position=150, id=".", ref="A",
alts="<DUP>", filter="PASS", info=var.get_info_as_string(),
format='INHERITANCE', sample='uncertain', gender="female",
mnv_code=None))