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())