class TestExomeCnvPy(unittest.TestCase):
""" test the Exome CNV filters
"""
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 test_add_cns_state(self):
""" test that add_cns_state() works correctly
"""
# meanl2r > 0 gives cns of 3
self.var.cnv.info["MEANLR2"] = "1"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "3")
self.var.cnv.info["MEANLR2"] = "0"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "3")
self.var.cnv.info["MEANLR2"] = "-0.1"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "1")
self.var.cnv.info["MEANLR2"] = "-2"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "1")
self.var.cnv.info["MEANLR2"] = "-2.1"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "0")
def test_fails_mad_ratio(self):
""" test that fails_mad_ratio() works correctly
"""
# check that var passes when MAD ratio > 5
self.var.cnv.info["MEANLR2"] = "0.5"
self.var.cnv.info["MADL2R"] = "0.02"
self.assertFalse(self.var.fails_mad_ratio())
# check that var passes when MAD ratio == 5
self.var.cnv.info["MEANLR2"] = "0.1"
self.var.cnv.info["MADL2R"] = "0.01"
self.assertFalse(self.var.fails_mad_ratio())
# check that var fails when MAD ratio < 5
self.var.cnv.info["MEANLR2"] = "0.09"
self.var.cnv.info["MADL2R"] = "0.01"
self.assertTrue(self.var.fails_mad_ratio())
# check that var fails when trying to divide by zero
self.var.cnv.info["MEANLR2"] = "0.2"
self.var.cnv.info["MADL2R"] = "0"
self.assertTrue(self.var.fails_mad_ratio())
def test_fails_meanlr2(self):
""" test that fails_meanlr2() works correctly
"""
# below the DUP threshold
self.var.cnv.genotype = 'DUP'
self.var.cnv.info["MEANLR2"] = "0.399"
self.assertTrue(self.var.fails_meanlr2())
# at the DUP threshold
self.var.cnv.info["MEANLR2"] = "0.4"
self.assertFalse(self.var.fails_meanlr2())
# above the DUP threshold
self.var.cnv.info["MEANLR2"] = "0.41"
self.assertFalse(self.var.fails_meanlr2())
# above the DEL threshold
self.var.cnv.genotype = 'DEL'
self.var.cnv.info["MEANLR2"] = "-0.4999"
self.assertTrue(self.var.fails_meanlr2())
# at the DEL threshold
self.var.cnv.info["MEANLR2"] = "-0.5"
self.assertFalse(self.var.fails_meanlr2())
# below the DEL threshold
self.var.cnv.info["MEANLR2"] = "-0.51"
self.assertFalse(self.var.fails_meanlr2())
def test_fails_population_frequency(self):
""" test that fails_population_frequency() works correctly
"""
# check that var passes when RC50INTERNALFREQ < 0.01
self.var.cnv.info["RC50INTERNALFREQ"] = "0.005"
self.assertFalse(self.var.fails_population_frequency())
# check that var passes when RC50INTERNALFREQ == 0.1
self.var.cnv.info["RC50INTERNALFREQ"] = "0.01"
self.assertFalse(self.var.fails_population_frequency())
# check that var fails when RC50INTERNALFREQ > 0.1
self.var.cnv.info["RC50INTERNALFREQ"] = "0.02"
self.assertTrue(self.var.fails_population_frequency())
def test_fails_convex_score(self):
""" test that fails_convex_score() works correctly
"""
# check that var passes when CONVEXSCORE > 7
self.var.cnv.info["CONVEXSCORE"] = "8"
self.assertFalse(self.var.fails_convex_score())
# check that var fails when CONVEXSCORE == 7
self.var.cnv.info["CONVEXSCORE"] = "7"
self.assertTrue(self.var.fails_convex_score())
# check that var fails when CONVEXSCORE < 7
self.var.cnv.info["CONVEXSCORE"] = "6"
self.assertTrue(self.var.fails_convex_score())
def test_fails_commmon_forwards(self):
""" test that fails_commmon_forwards() works correctly
"""
# check that var passes when COMMONFORWARDS < 0.8
self.var.cnv.info["COMMONFORWARDS"] = "0.0"
self.assertFalse(self.var.fails_commmon_forwards())
# check that var fails when COMMONFORWARDS == 0.8
self.var.cnv.info["COMMONFORWARDS"] = "0.8"
self.assertFalse(self.var.fails_commmon_forwards())
# check that var fails when COMMONFORWARDS > 0.8
self.var.cnv.info["COMMONFORWARDS"] = "0.9"
self.assertTrue(self.var.fails_commmon_forwards())
def test_fails_no_exons(self):
""" test that fails_no_exons() works correctly
"""
self.var.cnv.info["NUMBEREXONS"] = "1"
self.assertFalse(self.var.fails_no_exons())
self.var.cnv.info["NUMBEREXONS"] = "0"
self.assertTrue(self.var.fails_no_exons())
def test_fails_x_lr2(self):
"""test that fails_x_lr2() works correctly
"""
self.var.cnv.chrom = "X"
self.var.cnv.sum_x_lr2 = "-6000"
self.assertTrue(self.var.fails_x_lr2())
self.var.cnv.sum_x_lr2 = "8000"
self.assertTrue(self.var.fails_x_lr2())
self.var.cnv.sum_x_lr2 = "2000"
self.assertFalse(self.var.fails_x_lr2())
def test_fails_additional_filters(self):
"""test that fails_additional_filters() works correctly
"""
self.var.cnv.genotype = "DUP"
self.var.cnv.format["CIFER_INHERITANCE"] = "maternal_inh"
self.var.cnv.info["MEANLR2"] = "-2"
self.var.cnv.info["CONVEXSCORE"] = "10"
self.var.cnv.info["MADL2R"] = "0.2"
self.assertFalse(self.var.fails_additional_filters())
self.var.cnv.genotype = "DEL"
self.assertFalse(self.var.fails_additional_filters())
self.var.cnv.format["CIFER_INHERITANCE"] = "not_inherited"
self.assertTrue(self.var.fails_additional_filters())
self.var.cnv.info["MADL2R"] = "0.1"
self.assertTrue(self.var.fails_additional_filters())
self.var.cnv.info["MEANLR2"] = "-1"
self.assertFalse(self.var.fails_additional_filters())
self.var.cnv.info["CONVEXSCORE"] = "20"
self.assertFalse(self.var.fails_additional_filters())
def test_fails_cifer_inh(self):
"""test that CNVs in non-trios aren't filtered out on cifer false pos
but those in trios are filtered out
"""
self.var.cnv.has_parents = True
self.var.cnv.format["CIFER_INHERITANCE"] = "false_positive"
self.assertTrue(self.var.fails_cifer_inh())
self.var.cnv.has_parents = False
self.var.cnv.format["CIFER_INHERITANCE"] = "false_positive"
self.assertFalse(self.var.fails_cifer_inh())
class TestExomeCnvPy(unittest.TestCase):
""" test the Exome CNV filters
"""
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 test_add_cns_state(self):
""" test that add_cns_state() works correctly
"""
# meanl2r > 0 gives cns of 3
self.var.cnv.info["MEANLR2"] = "1"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "3")
self.var.cnv.info["MEANLR2"] = "0"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "3")
self.var.cnv.info["MEANLR2"] = "-0.1"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "1")
self.var.cnv.info["MEANLR2"] = "-2"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "1")
self.var.cnv.info["MEANLR2"] = "-2.1"
self.var.cnv.add_cns_state()
self.assertEqual(self.var.cnv.info["CNS"], "0")
def test_fails_mad_ratio(self):
""" test that fails_mad_ratio() works correctly
"""
# check that var passes when MAD ratio > 5
self.var.cnv.info["MEANLR2"] = "0.5"
self.var.cnv.info["MADL2R"] = "0.02"
self.assertFalse(self.var.fails_mad_ratio())
# check that var passes when MAD ratio == 5
self.var.cnv.info["MEANLR2"] = "0.1"
self.var.cnv.info["MADL2R"] = "0.01"
self.assertFalse(self.var.fails_mad_ratio())
# check that var fails when MAD ratio < 5
self.var.cnv.info["MEANLR2"] = "0.09"
self.var.cnv.info["MADL2R"] = "0.01"
self.assertTrue(self.var.fails_mad_ratio())
# check that var fails when trying to divide by zero
self.var.cnv.info["MEANLR2"] = "0.2"
self.var.cnv.info["MADL2R"] = "0"
self.assertTrue(self.var.fails_mad_ratio())
def test_fails_meanlr2(self):
""" test that fails_meanlr2() works correctly
"""
# below the DUP threshold
self.var.cnv.genotype = 'DUP'
self.var.cnv.info["MEANLR2"] = "0.399"
self.assertTrue(self.var.fails_meanlr2())
# at the DUP threshold
self.var.cnv.info["MEANLR2"] = "0.4"
self.assertFalse(self.var.fails_meanlr2())
# above the DUP threshold
self.var.cnv.info["MEANLR2"] = "0.41"
self.assertFalse(self.var.fails_meanlr2())
# above the DEL threshold
self.var.cnv.genotype = 'DEL'
self.var.cnv.info["MEANLR2"] = "-0.4999"
self.assertTrue(self.var.fails_meanlr2())
# at the DEL threshold
self.var.cnv.info["MEANLR2"] = "-0.5"
self.assertFalse(self.var.fails_meanlr2())
# below the DEL threshold
self.var.cnv.info["MEANLR2"] = "-0.51"
self.assertFalse(self.var.fails_meanlr2())
def test_fails_population_frequency(self):
""" test that fails_population_frequency() works correctly
"""
# check that var passes when RC50INTERNALFREQ < 0.01
self.var.cnv.info["RC50INTERNALFREQ"] = "0.005"
self.assertFalse(self.var.fails_population_frequency())
# check that var passes when RC50INTERNALFREQ == 0.1
self.var.cnv.info["RC50INTERNALFREQ"] = "0.01"
self.assertFalse(self.var.fails_population_frequency())
# check that var fails when RC50INTERNALFREQ > 0.1
self.var.cnv.info["RC50INTERNALFREQ"] = "0.02"
self.assertTrue(self.var.fails_population_frequency())
def test_fails_convex_score(self):
""" test that fails_convex_score() works correctly
"""
# check that var passes when CONVEXSCORE > 7
self.var.cnv.info["CONVEXSCORE"] = "8"
self.assertFalse(self.var.fails_convex_score())
# check that var fails when CONVEXSCORE == 7
self.var.cnv.info["CONVEXSCORE"] = "7"
self.assertTrue(self.var.fails_convex_score())
# check that var fails when CONVEXSCORE < 7
self.var.cnv.info["CONVEXSCORE"] = "6"
self.assertTrue(self.var.fails_convex_score())
def test_fails_commmon_forwards(self):
""" test that fails_commmon_forwards() works correctly
"""
# check that var passes when COMMONFORWARDS < 0.8
self.var.cnv.info["COMMONFORWARDS"] = "0.0"
self.assertFalse(self.var.fails_commmon_forwards())
# check that var fails when COMMONFORWARDS == 0.8
self.var.cnv.info["COMMONFORWARDS"] = "0.8"
self.assertFalse(self.var.fails_commmon_forwards())
# check that var fails when COMMONFORWARDS > 0.8
self.var.cnv.info["COMMONFORWARDS"] = "0.9"
self.assertTrue(self.var.fails_commmon_forwards())
def test_fails_no_exons(self):
""" test that fails_no_exons() works correctly
"""
self.var.cnv.info["NUMBEREXONS"] = "1"
self.assertFalse(self.var.fails_no_exons())
self.var.cnv.info["NUMBEREXONS"] = "0"
self.assertTrue(self.var.fails_no_exons())
def test_fails_x_lr2(self):
"""test that fails_x_lr2() works correctly
"""
self.var.cnv.chrom = "X"
self.var.cnv.sum_x_lr2 = "-6000"
self.assertTrue(self.var.fails_x_lr2())
self.var.cnv.sum_x_lr2 = "8000"
self.assertTrue(self.var.fails_x_lr2())
self.var.cnv.sum_x_lr2 = "2000"
self.assertFalse(self.var.fails_x_lr2())
def test_fails_additional_filters(self):
"""test that fails_additional_filters() works correctly
"""
self.var.cnv.genotype = "DUP"
self.var.cnv.format["CIFER_INHERITANCE"] = "maternal_inh"
self.var.cnv.info["MEANLR2"] = "-2"
self.var.cnv.info["CONVEXSCORE"] = "10"
self.var.cnv.info["MADL2R"] = "0.2"
self.assertFalse(self.var.fails_additional_filters())
self.var.cnv.genotype = "DEL"
self.assertFalse(self.var.fails_additional_filters())
self.var.cnv.format["CIFER_INHERITANCE"] = "not_inherited"
self.assertTrue(self.var.fails_additional_filters())
self.var.cnv.info["MADL2R"] = "0.1"
self.assertTrue(self.var.fails_additional_filters())
self.var.cnv.info["MEANLR2"] = "-1"
self.assertFalse(self.var.fails_additional_filters())
self.var.cnv.info["CONVEXSCORE"] = "20"
self.assertFalse(self.var.fails_additional_filters())
def test_fails_cifer_inh(self):
"""test that CNVs in non-trios aren't filtered out on cifer false pos
but those in trios are filtered out
"""
self.var.cnv.has_parents = True
self.var.cnv.format["CIFER_INHERITANCE"] = "false_positive"
self.assertTrue(self.var.fails_cifer_inh())
self.var.cnv.has_parents = False
self.var.cnv.format["CIFER_INHERITANCE"] = "false_positive"
self.assertFalse(self.var.fails_cifer_inh())
