class TestVariantCnvPy(unittest.TestCase):
""" unit testing of the CNV class
"""
def setUp(self):
""" define a default VcfInfo object
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "<DUP>"
filt = "PASS"
info = "HGNC=TEST;HGNC_ALL=TEST,OR5A1;CQ=missense_variant;" \
"CNSOLIDATE;WSCORE=0.5;CALLP=0.000;COMMONFORWARDS=0.000;" \
"MEANLR2=0.5;MADL2R=0.02;END=16000000;SVLEN=1000000"
keys = "inheritance:DP"
values = "deNovo:50"
sex = "F"
# set up a CNV object
self.var = CNV(chrom, pos, snp_id, ref, alt, filt, info=info,
format=keys, sample=values, gender=sex)
def test_set_genotype(self):
""" test that set_genotype() operates correctly
"""
# check that DUPs are set correctly
self.var.alt_alleles = ["<DUP>"]
self.var.set_genotype()
self.assertEqual(self.var.genotype, "DUP")
# check that DELs are set correctly
self.var.alt_alleles = ["<DEL>"]
self.var.set_genotype()
self.assertEqual(self.var.genotype, "DEL")
# check that other genotypes raise an error
self.var.alt_alleles = ["G"]
with self.assertRaises(ValueError):
self.var.set_genotype()
# and check that we raise an error for female Y chrom CNVs
self.var.chrom = "Y"
self.var._set_gender("F")
with self.assertRaises(ValueError):
self.var.set_genotype()
def test_set_genotype_pseudoautosomal(self):
""" test that set_genotype() works correctly in pseudoautosomal regions
"""
pseudoautosomal_region_start = 60002
pseudoautosomal_region_end = 2699520
# set a CNV that lies within a pseudoautosomal region
self.var.chrom = "X"
self.var.position = pseudoautosomal_region_start + 1000
self.var.info["END"] = pseudoautosomal_region_end - 1000
self.var._set_gender("F")
self.var.alt_alleles = ["<DUP>"]
self.var.set_genotype()
self.assertEqual(self.var.genotype, "DUP")
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
def test_get_range(self):
""" test that get_range() operates correctly
"""
# check that range is set correctly under normal function
self.var.position = 1000
self.var.info["END"] = "2000"
self.assertEqual(self.var.get_range(), (1000, 2000))
# check that range is set correctly when no info available
self.var.info = {}
self.assertEqual(self.var.get_range(), (1000, 11000))
def test_fix_gene_IDs(self):
""" test that fix_gene_IDs() works correctly
"""
self.var.known_genes = {"TEST": {"start": 1000, "end": 2000, "chrom": "5"}}
# make a CNV that will overlap with the known gene set
self.var.genes = [["TEST"]]
self.var.position = 1000
self.var.info["END"] = "1500"
# check that fixing gene names does not alter anything for a CNV in a
# single known gene
self.var.fix_gene_IDs()
self.assertEqual(self.var.genes, [["TEST"]])
# check that fixing gene names does not alter names not in the gene dict
self.var.genes = [["TEST", "TEST2"]]
self.var.fix_gene_IDs()
self.assertEqual(self.var.genes, [["TEST", "TEST2"]])
# check that fixing gene names drop name of genes where the name is in
# the known genes dict, and the CNV and gene do not overlap
self.var.position = 900
self.var.info["END"] = "950"
self.var.fix_gene_IDs()
self.assertEqual(self.var.genes, [[".", "TEST2"]])
# check that when we do not have any known genes, the gene names are
# unaltered
self.var.genes = [["TEST", "TEST2"]]
self.var.known_genes = None
self.var.fix_gene_IDs()
self.assertEqual(self.var.genes, [["TEST", "TEST2"]])
def test_set_gene_from_info_cnv(self):
""" test that set_add_gene_from_info() works correctly
"""
# make sure the known genes are None, otherwise sometimes the values
# from test_variant_info.py unit tests can bleed through. I'm not sure
# why!
self.var.known_genes = None
# check that HGNC takes precedence
self.var.info["HGNC"] = "A"
self.var.info["HGNC_ALL"] = "B"
genes = self.var.get_gene_from_info(self.var.info, self.var.alt_alleles, [])
self.assertEqual(genes, [["A"]])
# check that HGNC is used in the absence of HGNC_ALL
del self.var.info["HGNC"]
genes = self.var.get_gene_from_info(self.var.info, self.var.alt_alleles, [])
self.assertEqual(genes, [["B"]])
# check that when HGNC and HGNC_ALL are undefined, we can still include
# CNVs overlapping genes through NUMBERGENES > 0.
del self.var.info["HGNC_ALL"]
# first test for NUMBERGENES = 0
self.var.info["NUMBERGENES"] = 0
genes = self.var.get_gene_from_info(self.var.info, self.var.alt_alleles, [])
self.assertIsNone(genes)
# and then make sure we are correct for NUMBERGENES > 0
self.var.info["NUMBERGENES"] = 1
genes = self.var.get_gene_from_info(self.var.info, self.var.alt_alleles, [])
self.assertEqual(genes, [["."]])
# finally check for no HGNC, HGNC_ALL, or NUMBERGENES
del self.var.info["NUMBERGENES"]
genes = self.var.get_gene_from_info(self.var.info, self.var.alt_alleles, [])
self.assertEqual(genes, [["1:15000000"]])
def test_get_genes(self):
""" test that get_genes() works correctly
"""
self.var.genes = None
self.assertEqual(self.var.get_genes(), [])
self.var.genes = ["TEST"]
self.assertEqual(self.var.get_genes(), ["TEST"])
self.var.genes = ["TEST1", "TEST2"]
self.assertEqual(self.var.get_genes(), ["TEST1", "TEST2"])
self.var.genes = ["."]
self.assertEqual(self.var.get_genes(), ["."])
def test_fails_y_chrom_female(self):
""" test that passes_filters() works correctly for female Y chrom CNVs
"""
self.var.chrom = "Y"
self.var._set_gender("F")
self.assertFalse(self.var.passes_filters())
class TestVariantCnvPy(unittest.TestCase):
"""
"""
def setUp(self):
""" define a default VcfInfo object
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "<DUP>"
filt = "PASS"
# set up a SNV object, since SNV inherits VcfInfo
self.var = CNV(chrom, pos, snp_id, ref, alt, filt)
info = "HGNC=TEST;HGNC_ALL=TEST,OR5A1;CQ=missense_variant;CNSOLIDATE;WSCORE=0.5;CALLP=0.000;COMMONFORWARDS=0.000;MEANLR2=0.5;MADL2R=0.02;END=16000000;SVLEN=1000000"
format_keys = "inheritance:DP"
sample_values = "deNovo:50"
self.var.add_info(info)
self.var.add_format(format_keys, sample_values)
self.var.set_gender("F")
def test_set_genotype(self):
""" test that set_genotype() operates correctly
"""
# check that DUPs are set correctly
self.var.alt_allele = "<DUP>"
self.var.set_genotype()
self.assertEqual(self.var.genotype, "DUP")
# check that DELs are set correctly
self.var.alt_allele = "<DEL>"
self.var.set_genotype()
self.assertEqual(self.var.genotype, "DEL")
# check that other genotypes raise an error
self.var.alt_allele = "G"
with self.assertRaises(ValueError):
self.var.set_genotype()
# and check that we raise an error for female Y chrom CNVs
self.var.chrom = "Y"
self.var.set_gender("F")
with self.assertRaises(ValueError):
self.var.set_genotype()
def test_set_genotype_pseudoautosomal(self):
""" test that set_genotype() works correctly in pseudoautosomal regions
"""
pseudoautosomal_region_start = 60002
pseudoautosomal_region_end = 2699520
# set a CNV that lies within a pseudoautosomal region
self.var.chrom = "X"
self.var.position = pseudoautosomal_region_start + 1000
self.var.info["END"] = pseudoautosomal_region_end - 1000
self.var.set_gender("F")
self.var.alt_allele = "<DUP>"
self.var.set_genotype()
self.assertEqual(self.var.genotype, "DUP")
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
def test_get_range(self):
""" test that get_range() operates correctly
"""
# check that range is set correctly under normal function
self.var.position = 1000
self.var.info["END"] = "2000"
self.assertEqual(self.var.get_range(), (1000, 2000))
# check that range is set correctly when no info available
self.var.info = {}
self.assertEqual(self.var.get_range(), (1000, 11000))
def test_fix_gene_IDs(self):
""" test that fix_gene_IDs() works correctly
"""
self.var.known_genes = {"TEST": {"start": 1000, "end": 2000, "chrom": "5"}}
# make a CNV that will overlap with the known gene set
self.var.genes = ["TEST"]
self.var.position = 1000
self.var.info["END"] = "1500"
# check that fixing gene names does not alter anything for a CNV in a
# single known gene
self.var.fix_gene_IDs()
self.assertEqual(self.var.genes, ["TEST"])
# check that fixing gene names does not alter names not in the gene dict
self.var.genes = ["TEST", "TEST2"]
self.var.fix_gene_IDs()
self.assertEqual(self.var.genes, ["TEST", "TEST2"])
# check that fixing gene names drop name of genes where the name is in
# the known genes dict, and the CNV and gene do not overlap
self.var.position = 900
self.var.info["END"] = "950"
self.var.fix_gene_IDs()
self.assertEqual(self.var.genes, [".", "TEST2"])
# check that when we do not have any known genes, the gene names are
# unaltered
self.var.genes = ["TEST", "TEST2"]
self.var.known_genes = None
self.var.fix_gene_IDs()
self.assertEqual(self.var.genes, ["TEST", "TEST2"])
def test_set_gene_from_info_cnv(self):
""" test that set_add_gene_from_info() works correctly
"""
# make sure the known genes are None, otherwise sometimes the values
# from test_variant_info.py unit tests can bleed through. I'm not sure
# why!
self.var.known_genes = None
# check that HGNC takes precedence
self.var.info["HGNC"] = "A"
self.var.info["HGNC_ALL"] = "B"
self.var.set_gene_from_info()
self.assertEqual(self.var.genes, ["A"])
# check that HGNC is used in the absence of HGNC_ALL
del self.var.info["HGNC"]
self.var.set_gene_from_info()
self.assertEqual(self.var.genes, ["B"])
# check that when HGNC and HGNC_ALL are undefined, we can still include
# CNVs overlapping genes through NUMBERGENES > 0.
del self.var.info["HGNC_ALL"]
# first test for NUMBERGENES = 0
self.var.info["NUMBERGENES"] = 0
self.var.set_gene_from_info()
self.assertIsNone(self.var.genes)
# and then make sure we are correct for NUMBERGENES > 0
self.var.info["NUMBERGENES"] = 1
self.var.set_gene_from_info()
self.assertEqual(self.var.genes, ["."])
# finally check for no HGNC, HGNC_ALL, or NUMBERGENES
del self.var.info["NUMBERGENES"]
self.var.set_gene_from_info()
self.assertEqual(self.var.genes, "1:15000000")
def test_get_genes(self):
""" test that get_genes() works correctly
"""
self.var.genes = None
self.assertEqual(self.var.get_genes(), [])
self.var.genes = ["TEST"]
self.assertEqual(self.var.get_genes(), ["TEST"])
self.var.genes = ["TEST1", "TEST2"]
self.assertEqual(self.var.get_genes(), ["TEST1", "TEST2"])
self.var.genes = ["."]
self.assertEqual(self.var.get_genes(), ["."])
def test_fails_y_chrom_female(self):
""" test that passes_filters() works correctly for female Y chrom CNVs
"""
self.var.chrom = "Y"
self.var.set_gender("F")
self.assertFalse(self.var.passes_filters())
class TestVariantCnvPy(unittest.TestCase):
""" unit testing of the CNV class
"""
def setUp(self):
""" define a default VcfInfo object
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "<DUP>"
qual = "1000"
filt = "PASS"
info = "HGNC=TEST;HGNC_ALL=TEST,OR5A1;CQ=missense_variant;" \
"CNSOLIDATE;WSCORE=0.5;CALLP=0.000;COMMONFORWARDS=0.000;" \
"MEANLR2=0.5;MADL2R=0.02;END=16000000;SVLEN=1000000"
keys = "inheritance:DP"
values = "deNovo:50"
sex = "F"
# set up a CNV object
self.var = CNV(chrom,
pos,
snp_id,
ref,
alt,
qual,
filt,
info=info,
format=keys,
sample=values,
gender=sex)
def test_set_genotype(self):
""" test that set_genotype() operates correctly
"""
# check that DUPs are set correctly
self.var.alt_alleles = ["<DUP>"]
self.var.set_genotype()
self.assertEqual(self.var.genotype, "DUP")
# check that DELs are set correctly
self.var.alt_alleles = ["<DEL>"]
self.var.set_genotype()
self.assertEqual(self.var.genotype, "DEL")
# check that other genotypes raise an error
self.var.alt_alleles = ["G"]
with self.assertRaises(ValueError):
self.var.set_genotype()
# and check that we raise an error for female Y chrom CNVs
self.var.chrom = "Y"
self.var._set_gender("F")
with self.assertRaises(ValueError):
self.var.set_genotype()
def test_set_genotype_pseudoautosomal(self):
""" test that set_genotype() works correctly in pseudoautosomal regions
"""
pseudoautosomal_region_start = 60002
pseudoautosomal_region_end = 2699520
# set a CNV that lies within a pseudoautosomal region
self.var.chrom = "X"
self.var.position = pseudoautosomal_region_start + 1000
self.var.info["END"] = pseudoautosomal_region_end - 1000
self.var._set_gender("F")
self.var.alt_alleles = ["<DUP>"]
self.var.set_genotype()
self.assertEqual(self.var.genotype, "DUP")
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
def test_get_range(self):
""" test that get_range() operates correctly
"""
# check that range is set correctly under normal function
self.var.position = 1000
self.var.info["END"] = "2000"
self.assertEqual(self.var.get_range(), (1000, 2000))
# check that range is set correctly when no info available
self.var.info = {}
self.assertEqual(self.var.get_range(), (1000, 11000))
def test_fix_gene_IDs(self):
""" test that fix_gene_IDs() works correctly
"""
self.var.known_genes = {
"TEST": {
"start": 1000,
"end": 2000,
"chrom": "5"
}
}
# make a CNV that will overlap with the known gene set
self.var.info.symbols = [Symbols(info={'HGNC_ID': 'TEST'}, idx=0)]
self.var.position = 1000
self.var.info["END"] = "1500"
# check that fixing gene names does not alter anything for a CNV in a
# single known gene
self.var.fix_gene_IDs()
self.assertEqual(self.var.info.get_genes(), [['TEST']])
# check that fixing gene names does not alter names not in the gene dict
self.var.info.symbols = [
Symbols(info={'HGNC_ID': 'TEST|TEST2'}, idx=0)
]
self.var.fix_gene_IDs()
self.assertEqual(self.var.info.get_genes(), [['TEST', 'TEST2']])
# check that fixing gene names drop name of genes where the name is in
# the known genes dict, and the CNV and gene do not overlap
self.var.position = 900
self.var.info["END"] = "950"
self.var.fix_gene_IDs()
self.assertEqual(self.var.info.get_genes(), [[None, 'TEST2']])
# check that when we do not have any known genes, the gene names are
# unaltered
self.var.info.symbols = [
Symbols(info={'HGNC_ID': 'TEST|TEST2'}, idx=0)
]
self.var.known_genes = None
self.var.fix_gene_IDs()
self.assertEqual(self.var.info.get_genes(), [['TEST', 'TEST2']])
def test_set_gene_from_info_cnv(self):
""" test that set_add_gene_from_info() works correctly
"""
# make sure the known genes are None, otherwise sometimes the values
# from test_variant_info.py unit tests can bleed through. I'm not sure
# why!
self.var.known_genes = None
# check that HGNC takes precedence
self.var.info["HGNC"] = "A"
genes = self.var.info.parse_gene_symbols(self.var.alt_alleles, [])
self.assertEqual(genes, [Symbols(info={'HGNC': 'A'}, idx=0)])
# check that HGNC_ALL doesn't affect anything
self.var.info["HGNC_ALL"] = "B"
del self.var.info["HGNC"]
genes = self.var.info.parse_gene_symbols(self.var.alt_alleles, [])
self.assertEqual(genes, [Symbols(info={}, idx=0)])
def test_get_genes(self):
""" test that get_genes() works correctly
"""
self.var.info.symbols = [Symbols(info={}, idx=0)]
self.assertEqual(self.var.info.get_genes(), [[]])
self.var.info.symbols = [Symbols(info={'HGNC': 'TEST'}, idx=0)]
self.assertEqual(self.var.info.get_genes(), [["TEST"]])
self.var.info.symbols = [Symbols(info={'HGNC': 'TEST1|TEST2'}, idx=0)]
self.assertEqual(self.var.info.get_genes(), [["TEST1", "TEST2"]])
self.var.info.symbols = [Symbols(info={'HGNC': '.'}, idx=0)]
self.assertEqual(self.var.info.get_genes(), [[None]])
def test_fails_y_chrom_female(self):
""" test that passes_filters() works correctly for female Y chrom CNVs
"""
self.var.chrom = "Y"
self.var._set_gender("F")
self.assertFalse(self.var.passes_filters())