def setUp(self):
""" define a default variant (currently a SNV)
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "G"
filt = "PASS"
self.var = Variant(chrom, pos, snp_id, ref, alt, filt)
def setUp(self):
""" define a default variant (currently a SNV)
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "G"
qual = "1000"
filt = "PASS"
info = 'AC=1;HGNC=TEST'
keys = 'GT:DP:AD'
sample = '0/1:40:10,10'
self.var = Variant(chrom, pos, snp_id, ref, alt, qual, filt, info,
keys, sample)
def setUp(self):
""" define a default variant (currently a SNV)
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "G"
filt = "PASS"
self.var = Variant(chrom, pos, snp_id, ref, alt, filt)
class TestVariantPy(unittest.TestCase):
""" test Variant objects and their methods
"""
def setUp(self):
""" define a default variant (currently a SNV)
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "G"
qual = "1000"
filt = "PASS"
info = 'AC=1;HGNC=TEST'
keys = 'GT:DP:AD'
sample = '0/1:40:10,10'
self.var = Variant(chrom, pos, snp_id, ref, alt, qual, filt, info,
keys, sample)
def test_set_gender_unknown(self):
""" tests set_gender(), and its implications on the inheritance type
"""
# raise error for unknown gender
with self.assertRaises(ValueError):
self.var._set_gender("unknown")
def test_set_gender_autosomal(self):
"""test gender on autosomal chroms
"""
# check all the legitimate gender codes
gender_codes = ["1", "m", "M", "male", "2", "f", "F", "female"]
for gender in gender_codes:
self.var._set_gender(gender)
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
def test_set_gender_allosomal(self):
""" test gender on the X chromosome
"""
# check the allosomal chroms
self.var.chrom = "X"
self.var._set_gender("male")
self.assertEqual(self.var.get_inheritance_type(), "XChrMale")
self.var._set_gender("female")
self.assertEqual(self.var.get_inheritance_type(), "XChrFemale")
# check the allosomal chroms
self.var.chrom = "Y"
self.var._set_gender("male")
self.assertEqual(self.var.get_inheritance_type(), "YChrMale")
self.var._set_gender("female")
self.assertEqual(self.var.get_inheritance_type(), "YChrFemale")
def test_set_gender_pseudoautosomal(self):
""" test gender on a pseudoautosomal region
"""
# now check a variant in the pseudoautosomal regions
self.var.chrom = "X"
self.var.position = 2699510
self.var._set_gender("male")
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
self.var._set_gender("female")
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
def test_get_chrom(self):
""" tests that the chrom returns correctly
"""
# check that the chrom is the default chrom
self.assertEqual(self.var.get_chrom(), "1")
# check that we can change the chrom and it still returns correctly
self.var.chrom = "X"
self.assertEqual(self.var.get_chrom(), "X")
def test_get_position(self):
""" tests that the position returns correctly
"""
# check the default position
self.assertEqual(self.var.get_position(), 15000000)
# check that we can change the chrom and it still returns correctly
self.var.position = 123456789
self.assertEqual(self.var.get_position(), 123456789)
def test_get_mutation_id(self):
""" test that the mutation ID is parsed correctly
"""
var = self.var
# check a null ID value
var.set_mutation_id(".")
self.assertEqual(var.get_mutation_id(), "NA")
# check a rsID value
var.set_mutation_id("rs12546")
self.assertEqual(var.get_mutation_id(), "NA")
# check a rsID and a mutation ID
var.set_mutation_id("rs12546&CM0001")
self.assertEqual(var.get_mutation_id(), "CM0001")
# check multiple mutation IDs
var.set_mutation_id("CM0001&CM0002")
self.assertEqual(var.get_mutation_id(), "CM0001,CM0002")
def test_get_vcf_line(self):
""" tests that the vcf line string returns correctly
"""
vcf_line = [
"1", "15000000", ".", "A", "G", "50", "PASS", "AB=0.41;AC=1;AN=2",
"GT:gatk_PL:GQ", "0/1:736,0,356:99"
]
self.var.add_vcf_line(vcf_line)
self.assertEqual(self.var.get_vcf_line(), vcf_line)
def test_get_low_depth_alleles(self):
''' test that get_low_depth_alleles() works correctly
'''
# check with a single allele whre it is non-zero
self.var.info = Info('AC=1')
alts = ('C', )
self.assertEqual(self.var.get_low_depth_alleles('G', alts), [])
# check with a single allele with zero count
self.var.info = Info('AC=0')
alts = ('C', )
self.assertEqual(self.var.get_low_depth_alleles('G', alts), ['C'])
# check with multiallelic, where both are nonzero
self.var.info = Info('AC=1,1')
self.var.format = {'AD': '5,10,10'}
alts = ('C', 'G')
self.assertEqual(self.var.get_low_depth_alleles('G', alts), [])
# check with multiallelic, where one a has zero count
self.var.info = Info('AC=1,0')
self.var.format = {'AD': '5,10,10'}
alts = ('C', 'G')
self.assertEqual(self.var.get_low_depth_alleles('G', alts), ['G'])
def test_get_low_depth_alleles_bad_indel(self):
''' test that get_low_depth_alleles() works for indels with depth=1
'''
# check with multiallelic, where all should pass, since none are indels
self.var.info = Info('AC=1,1')
self.var.format = {'AD': '5,10,1'}
alts = ('C', 'G')
self.assertEqual(self.var.get_low_depth_alleles('G', alts), [])
# but if we have an indel alt, and the corresponding depth is bad, fail
alts = ('C', 'GG')
self.assertEqual(self.var.get_low_depth_alleles('G', alts), ['GG'])
class TestVariantPy(unittest.TestCase):
""" test Variant objects and their methods
"""
def setUp(self):
""" define a default variant (currently a SNV)
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "G"
filt = "PASS"
self.var = Variant(chrom, pos, snp_id, ref, alt, filt)
def test_set_gender_unknown(self):
""" tests set_gender(), and its implications on the inheritance type
"""
# raise error for unknown gender
with self.assertRaises(ValueError):
self.var.set_gender("unknown")
def test_set_gender_autosomal(self):
"""test gender on autosomal chroms
"""
# check all the legitimate gender codes
gender_codes = ["1", "m", "M", "male", "2", "f", "F", "female"]
for gender in gender_codes:
self.var.set_gender(gender)
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
def test_set_gender_allosomal(self):
""" test gender on the X chromosome
"""
# check the allosomal chroms
self.var.chrom = "X"
self.var.set_gender("male")
self.assertEqual(self.var.get_inheritance_type(), "XChrMale")
self.var.set_gender("female")
self.assertEqual(self.var.get_inheritance_type(), "XChrFemale")
# check the allosomal chroms
self.var.chrom = "Y"
self.var.set_gender("male")
self.assertEqual(self.var.get_inheritance_type(), "YChrMale")
self.var.set_gender("female")
self.assertEqual(self.var.get_inheritance_type(), "YChrFemale")
def test_set_gender_pseudoautosomal(self):
""" test gender on a pseudoautosomal region
"""
# now check a variant in the pseudoautosomal regions
self.var.chrom = "X"
self.var.position = 2699510
self.var.set_gender("male")
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
self.var.set_gender("female")
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
def test_get_chrom(self):
""" tests that the chrom returns correctly
"""
# check that the chrom is the default chrom
self.assertEqual(self.var.get_chrom(), "1")
# check that we can change the chrom and it still returns correctly
self.var.chrom = "X"
self.assertEqual(self.var.get_chrom(), "X")
def test_get_position(self):
""" tests that the position returns correctly
"""
# check the default position
self.assertEqual(self.var.get_position(), 15000000)
# check that we can change the chrom and it still returns correctly
self.var.position = 123456789
self.assertEqual(self.var.get_position(), 123456789)
def test_get_mutation_id(self):
""" test that the mutation ID is parsed correctly
"""
var = self.var
# check a null ID value
var.set_mutation_id(".")
self.assertEqual(var.get_mutation_id(), "NA")
# check a rsID value
var.set_mutation_id("rs12546")
self.assertEqual(var.get_mutation_id(), "NA")
# check a rsID and a mutation ID
var.set_mutation_id("rs12546&CM0001")
self.assertEqual(var.get_mutation_id(), "CM0001")
# check multiple mutation IDs
var.set_mutation_id("CM0001&CM0002")
self.assertEqual(var.get_mutation_id(), "CM0001,CM0002")
def test_get_vcf_line(self):
""" tests that the vcf line string returns correctly
"""
vcf_line = ["1", "15000000", ".", "A", "G", "50", "PASS", "AB=0.41;AC=1;AN=2", "GT:gatk_PL:GQ", "0/1:736,0,356:99"]
self.var.add_vcf_line(vcf_line)
self.assertEqual(self.var.get_vcf_line(), vcf_line)
class TestVariantPy(unittest.TestCase):
""" test Variant objects and their methods
"""
def setUp(self):
""" define a default variant (currently a SNV)
"""
chrom = "1"
pos = "15000000"
snp_id = "."
ref = "A"
alt = "G"
filt = "PASS"
self.var = Variant(chrom, pos, snp_id, ref, alt, filt)
def test_set_gender_unknown(self):
""" tests set_gender(), and its implications on the inheritance type
"""
# raise error for unknown gender
with self.assertRaises(ValueError):
self.var.set_gender("unknown")
def test_set_gender_autosomal(self):
"""test gender on autosomal chroms
"""
# check all the legitimate gender codes
gender_codes = ["1", "m", "M", "male", "2", "f", "F", "female"]
for gender in gender_codes:
self.var.set_gender(gender)
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
def test_set_gender_allosomal(self):
""" test gender on the X chromosome
"""
# check the allosomal chroms
self.var.chrom = "X"
self.var.set_gender("male")
self.assertEqual(self.var.get_inheritance_type(), "XChrMale")
self.var.set_gender("female")
self.assertEqual(self.var.get_inheritance_type(), "XChrFemale")
# check the allosomal chroms
self.var.chrom = "Y"
self.var.set_gender("male")
self.assertEqual(self.var.get_inheritance_type(), "YChrMale")
self.var.set_gender("female")
self.assertEqual(self.var.get_inheritance_type(), "YChrFemale")
def test_set_gender_pseudoautosomal(self):
""" test gender on a pseudoautosomal region
"""
# now check a variant in the pseudoautosomal regions
self.var.chrom = "X"
self.var.position = 2699510
self.var.set_gender("male")
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
self.var.set_gender("female")
self.assertEqual(self.var.get_inheritance_type(), "autosomal")
def test_get_chrom(self):
""" tests that the chrom returns correctly
"""
# check that the chrom is the default chrom
self.assertEqual(self.var.get_chrom(), "1")
# check that we can change the chrom and it still returns correctly
self.var.chrom = "X"
self.assertEqual(self.var.get_chrom(), "X")
def test_get_position(self):
""" tests that the position returns correctly
"""
# check the default position
self.assertEqual(self.var.get_position(), 15000000)
# check that we can change the chrom and it still returns correctly
self.var.position = 123456789
self.assertEqual(self.var.get_position(), 123456789)
def test_get_mutation_id(self):
""" test that the mutation ID is parsed correctly
"""
var = self.var
# check a null ID value
var.set_mutation_id(".")
self.assertEqual(var.get_mutation_id(), "NA")
# check a rsID value
var.set_mutation_id("rs12546")
self.assertEqual(var.get_mutation_id(), "NA")
# check a rsID and a mutation ID
var.set_mutation_id("rs12546&CM0001")
self.assertEqual(var.get_mutation_id(), "CM0001")
# check multiple mutation IDs
var.set_mutation_id("CM0001&CM0002")
self.assertEqual(var.get_mutation_id(), "CM0001,CM0002")
def test_get_vcf_line(self):
""" tests that the vcf line string returns correctly
"""
vcf_line = [
"1", "15000000", ".", "A", "G", "50", "PASS", "AB=0.41;AC=1;AN=2",
"GT:gatk_PL:GQ", "0/1:736,0,356:99"
]
self.var.add_vcf_line(vcf_line)
self.assertEqual(self.var.get_vcf_line(), vcf_line)
