class TestAcghCnvPy(unittest.TestCase):
""" test the ACGH CNV filters
"""
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_fails_mad_ratio(self):
""" test that fails_mad_ratio() works correctly.
"""
# check that var passes when MAD ratio >= 15
self.var.cnv.info["MEANLR2"] = "0.3"
self.var.cnv.info["MADL2R"] = "0.02"
self.assertFalse(self.var.fails_mad_ratio())
# check that var fails when MAD ratio < 10
self.var.cnv.info["MEANLR2"] = "0.29"
self.var.cnv.info["MADL2R"] = "0.03"
self.assertTrue(self.var.fails_mad_ratio())
# check that var passes when MAD ratio == 0
self.var.cnv.info["MEANLR2"] = "0.3"
self.var.cnv.info["MADL2R"] = float("inf")
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())
# check that var passes when the fields are NA
self.var.cnv.info["MEANLR2"] = "0.2"
self.var.cnv.info["MADL2R"] = "NA"
self.assertFalse(self.var.fails_mad_ratio())
def test_fails_wscore(self):
""" test that fails_wscore() works correctly
"""
# check that var passes when WSCORE > 0.45
self.var.cnv.info["WSCORE"] = "0.45"
self.assertFalse(self.var.fails_wscore())
# check that var fails when WSCORE < 0.45
self.var.cnv.info["WSCORE"] = "0.449"
self.assertTrue(self.var.fails_wscore())
def test_fails_callp(self):
""" test that fails_callp() works correctly
"""
# check that var passes when CALLP < 0.01
self.var.cnv.info["CALLP"] = "0.0"
self.assertFalse(self.var.fails_callp())
# check that var passes when CALLP == 0.01
self.var.cnv.info["CALLP"] = "0.01"
self.assertFalse(self.var.fails_callp())
# check that var fails when CALLP > 0.01
self.var.cnv.info["CALLP"] = "0.0101"
self.assertTrue(self.var.fails_callp())
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_mean_lr2_dup(self):
""" test that fails_mean_lr2() works correctly on duplications
"""
# set the var as a duplication
self.var.cnv.alt_alleles = ["<DUP>"]
self.var.cnv.set_genotype()
# check that dup passes with MEANLR2 > 0.4
self.var.cnv.info["MEANLR2"] = "0.4"
self.assertFalse(self.var.fails_meanlr2())
# check that dup passes with MEANLR2 < 0.4
self.var.cnv.info["MEANLR2"] = "0.399"
self.assertTrue(self.var.fails_meanlr2())
def test_fails_mean_lr2_del(self):
""" test that fails_mean_lr2() works correctly on deletions
"""
# set the var as a deletion
self.var.cnv.alt_alleles = ["<DEL>"]
self.var.cnv.set_genotype()
# check that del passes with MEANLR2 < -0.5
self.var.cnv.info["MEANLR2"] = "-0.5"
self.assertFalse(self.var.fails_meanlr2())
# check that del fails with MEANLR2 > -0.41
self.var.cnv.info["MEANLR2"] = "-0.499"
self.assertTrue(self.var.fails_meanlr2())
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_frequency(self):
""" test that fails_frequency() works correctly
"""
# a low population frequency will pass
self.var.cnv.info["ACGH_RC_FREQ50"] = "0.01"
self.assertFalse(self.var.fails_frequency())
# a high population frequency will fail
self.var.cnv.info["ACGH_RC_FREQ50"] = "0.011"
self.assertTrue(self.var.fails_frequency())
# if population frequency information is unavailable, it should pass,
# since this suggests the frequency is 0.
del self.var.cnv.info["ACGH_RC_FREQ50"]
self.assertFalse(self.var.fails_frequency())
def test_fails_cifer_inh(self):
""" test that fails_cifer_inh() works correctly
"""
# CNVs annotated as not_inherited, or inherited will pass
self.var.cnv.format["CIFER_INHERITANCE"] = "not_inherited"
self.assertFalse(self.var.fails_cifer_inh())
# CNVs annotated as false_positive will fail
self.var.cnv.format["CIFER_INHERITANCE"] = "false_positive"
self.assertTrue(self.var.fails_cifer_inh())
class TestAcghCnvPy(unittest.TestCase):
""" test the ACGH CNV filters
"""
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
cnv = CNV(chrom, pos, snp_id, ref, alt, filt)
self.var = ACGH_CNV(cnv)
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.cnv.add_info(info)
self.var.cnv.add_format(format_keys, sample_values)
self.var.cnv.set_gender("F")
def test_fails_mad_ratio(self):
""" test that fails_mad_ratio() works correctly
"""
# check that var passes when MAD ratio > 15
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 == 15
self.var.cnv.info["MEANLR2"] = "0.3"
self.var.cnv.info["MADL2R"] = "0.02"
self.assertFalse(self.var.fails_mad_ratio())
# check that var fails when MAD ratio < 15
self.var.cnv.info["MEANLR2"] = "0.2"
self.var.cnv.info["MADL2R"] = "0.02"
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_wscore(self):
""" test that fails_wscore() works correctly
"""
# check that var passes when WSCORE > 0.4
self.var.cnv.info["WSCORE"] = "0.5"
self.assertFalse(self.var.fails_wscore())
# check that var passes when WSCORE == 0.4
self.var.cnv.info["WSCORE"] = "0.4"
self.assertFalse(self.var.fails_wscore())
# check that var fails when WSCORE > 0.4
self.var.cnv.info["WSCORE"] = "0.399"
self.assertTrue(self.var.fails_wscore())
def test_fails_callp(self):
""" test that fails_callp() works correctly
"""
# check that var passes when CALLP < 0.01
self.var.cnv.info["CALLP"] = "0.0"
self.assertFalse(self.var.fails_callp())
# check that var passes when CALLP == 0.01
self.var.cnv.info["CALLP"] = "0.01"
self.assertFalse(self.var.fails_callp())
# check that var fails when CALLP > 0.01
self.var.cnv.info["CALLP"] = "0.0101"
self.assertTrue(self.var.fails_callp())
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_mean_lr2_dup(self):
""" test that fails_mean_lr2() works correctly on duplications
"""
# set the var as a duplication
self.var.cnv.alt_allele = "<DUP>"
self.var.cnv.set_genotype()
# check that dup passes with MEANLR2 > 0.36
self.var.cnv.info["MEANLR2"] = "0.4"
self.assertFalse(self.var.fails_meanlr2())
# check that dup passes with MEANLR2 == 0.36
self.var.cnv.info["MEANLR2"] = "0.36"
self.assertFalse(self.var.fails_meanlr2())
# check that dup passes with MEANLR2 < 0.36
self.var.cnv.info["MEANLR2"] = "0.359"
self.assertTrue(self.var.fails_meanlr2())
def test_fails_mean_lr2_del(self):
""" test that fails_mean_lr2() works correctly on deletions
"""
# set the var as a deletion
self.var.cnv.alt_allele = "<DEL>"
self.var.cnv.set_genotype()
# check that del passes with MEANLR2 < -0.41
self.var.cnv.info["MEANLR2"] = "-0.5"
self.assertFalse(self.var.fails_meanlr2())
# check that del passes with MEANLR2 == -0.41
self.var.cnv.info["MEANLR2"] = "-0.41"
self.assertFalse(self.var.fails_meanlr2())
# check that del passes with MEANLR2 > -0.41
self.var.cnv.info["MEANLR2"] = "-0.409"
self.assertTrue(self.var.fails_meanlr2())
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())
class TestAcghCnvPy(unittest.TestCase):
""" test the ACGH CNV filters
"""
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
cnv = CNV(chrom, pos, snp_id, ref, alt, filt)
self.var = ACGH_CNV(cnv)
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.cnv.add_info(info)
self.var.cnv.add_format(format_keys, sample_values)
self.var.cnv.set_gender("F")
def test_fails_mad_ratio(self):
""" test that fails_mad_ratio() works correctly.
"""
# check that var passes when MAD ratio > 0
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 == 0
self.var.cnv.info["MEANLR2"] = "0.3"
self.var.cnv.info["MADL2R"] = float("inf")
self.assertFalse(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_wscore(self):
""" test that fails_wscore() works correctly
"""
# check that var passes when WSCORE > 0.4
self.var.cnv.info["WSCORE"] = "0.5"
self.assertFalse(self.var.fails_wscore())
# check that var passes when WSCORE == 0.4
self.var.cnv.info["WSCORE"] = "0.4"
self.assertFalse(self.var.fails_wscore())
# check that var fails when WSCORE > 0.4
self.var.cnv.info["WSCORE"] = "0.399"
self.assertTrue(self.var.fails_wscore())
def test_fails_callp(self):
""" test that fails_callp() works correctly
"""
# check that var passes when CALLP < 0.01
self.var.cnv.info["CALLP"] = "0.0"
self.assertFalse(self.var.fails_callp())
# check that var passes when CALLP == 0.01
self.var.cnv.info["CALLP"] = "0.01"
self.assertFalse(self.var.fails_callp())
# check that var fails when CALLP > 0.01
self.var.cnv.info["CALLP"] = "0.0101"
self.assertTrue(self.var.fails_callp())
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_mean_lr2_dup(self):
""" test that fails_mean_lr2() works correctly on duplications
"""
# set the var as a duplication
self.var.cnv.alt_allele = "<DUP>"
self.var.cnv.set_genotype()
# check that dup passes with MEANLR2 > 0.36
self.var.cnv.info["MEANLR2"] = "0.4"
self.assertFalse(self.var.fails_meanlr2())
# check that dup passes with MEANLR2 == 0.36
self.var.cnv.info["MEANLR2"] = "0.36"
self.assertFalse(self.var.fails_meanlr2())
# check that dup passes with MEANLR2 < 0.36
self.var.cnv.info["MEANLR2"] = "0.359"
self.assertTrue(self.var.fails_meanlr2())
def test_fails_mean_lr2_del(self):
""" test that fails_mean_lr2() works correctly on deletions
"""
# set the var as a deletion
self.var.cnv.alt_allele = "<DEL>"
self.var.cnv.set_genotype()
# check that del passes with MEANLR2 < -0.41
self.var.cnv.info["MEANLR2"] = "-0.5"
self.assertFalse(self.var.fails_meanlr2())
# check that del passes with MEANLR2 == -0.41
self.var.cnv.info["MEANLR2"] = "-0.41"
self.assertFalse(self.var.fails_meanlr2())
# check that del passes with MEANLR2 > -0.41
self.var.cnv.info["MEANLR2"] = "-0.409"
self.assertTrue(self.var.fails_meanlr2())
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_frequency(self):
""" test that fails_frequency() works correctly
"""
# a low population frequency will pass
self.var.cnv.info["ACGH_RC_FREQ50"] = "0.01"
self.assertFalse(self.var.fails_frequency())
# a high population frequency will fail
self.var.cnv.info["ACGH_RC_FREQ50"] = "0.011"
self.assertTrue(self.var.fails_frequency())
# if population frequency information is unavailable, it should pass,
# since this suggests the frequency is 0.
del self.var.cnv.info["ACGH_RC_FREQ50"]
self.assertFalse(self.var.fails_frequency())
def test_fails_cifer_inh(self):
""" test that fails_cifer_inh() works correctly
"""
# CNVs annotated as not_inherited, or inherited will pass
self.var.cnv.format["CIFER_INHERITANCE"] = "not_inherited"
self.assertFalse(self.var.fails_cifer_inh())
# CNVs annotated as false_positive will fail
self.var.cnv.format["CIFER_INHERITANCE"] = "false_positive"
self.assertTrue(self.var.fails_cifer_inh())
class TestAcghCnvPy(unittest.TestCase):
""" test the ACGH CNV filters
"""
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_fails_mad_ratio(self):
""" test that fails_mad_ratio() works correctly.
"""
# check that var passes when MAD ratio >= 15
self.var.cnv.info["MEANLR2"] = "0.3"
self.var.cnv.info["MADL2R"] = "0.02"
self.assertFalse(self.var.fails_mad_ratio())
# check that var fails when MAD ratio < 10
self.var.cnv.info["MEANLR2"] = "0.29"
self.var.cnv.info["MADL2R"] = "0.03"
self.assertTrue(self.var.fails_mad_ratio())
# check that var passes when MAD ratio == 0
self.var.cnv.info["MEANLR2"] = "0.3"
self.var.cnv.info["MADL2R"] = float("inf")
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())
# check that var passes when the fields are NA
self.var.cnv.info["MEANLR2"] = "0.2"
self.var.cnv.info["MADL2R"] = "NA"
self.assertFalse(self.var.fails_mad_ratio())
def test_fails_wscore(self):
""" test that fails_wscore() works correctly
"""
# check that var passes when WSCORE > 0.45
self.var.cnv.info["WSCORE"] = "0.45"
self.assertFalse(self.var.fails_wscore())
# check that var fails when WSCORE < 0.45
self.var.cnv.info["WSCORE"] = "0.449"
self.assertTrue(self.var.fails_wscore())
def test_fails_callp(self):
""" test that fails_callp() works correctly
"""
# check that var passes when CALLP < 0.01
self.var.cnv.info["CALLP"] = "0.0"
self.assertFalse(self.var.fails_callp())
# check that var passes when CALLP == 0.01
self.var.cnv.info["CALLP"] = "0.01"
self.assertFalse(self.var.fails_callp())
# check that var fails when CALLP > 0.01
self.var.cnv.info["CALLP"] = "0.0101"
self.assertTrue(self.var.fails_callp())
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_mean_lr2_dup(self):
""" test that fails_mean_lr2() works correctly on duplications
"""
# set the var as a duplication
self.var.cnv.alt_alleles = ["<DUP>"]
self.var.cnv.set_genotype()
# check that dup passes with MEANLR2 > 0.4
self.var.cnv.info["MEANLR2"] = "0.4"
self.assertFalse(self.var.fails_meanlr2())
# check that dup passes with MEANLR2 < 0.4
self.var.cnv.info["MEANLR2"] = "0.399"
self.assertTrue(self.var.fails_meanlr2())
def test_fails_mean_lr2_del(self):
""" test that fails_mean_lr2() works correctly on deletions
"""
# set the var as a deletion
self.var.cnv.alt_alleles = ["<DEL>"]
self.var.cnv.set_genotype()
# check that del passes with MEANLR2 < -0.5
self.var.cnv.info["MEANLR2"] = "-0.5"
self.assertFalse(self.var.fails_meanlr2())
# check that del fails with MEANLR2 > -0.41
self.var.cnv.info["MEANLR2"] = "-0.499"
self.assertTrue(self.var.fails_meanlr2())
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_frequency(self):
""" test that fails_frequency() works correctly
"""
# a low population frequency will pass
self.var.cnv.info["ACGH_RC_FREQ50"] = "0.01"
self.assertFalse(self.var.fails_frequency())
# a high population frequency will fail
self.var.cnv.info["ACGH_RC_FREQ50"] = "0.011"
self.assertTrue(self.var.fails_frequency())
# if population frequency information is unavailable, it should pass,
# since this suggests the frequency is 0.
del self.var.cnv.info["ACGH_RC_FREQ50"]
self.assertFalse(self.var.fails_frequency())
def test_fails_cifer_inh(self):
""" test that fails_cifer_inh() works correctly
"""
# CNVs annotated as not_inherited, or inherited will pass
self.var.cnv.format["CIFER_INHERITANCE"] = "not_inherited"
self.assertFalse(self.var.fails_cifer_inh())
# CNVs annotated as false_positive will fail
self.var.cnv.format["CIFER_INHERITANCE"] = "false_positive"
self.assertTrue(self.var.fails_cifer_inh())
