class TestVcfToBedpeConverter(TestCase):
def setUp(self):
self.converter = VcfToBedpeConverter()
header_lines = [
'##fileformat=VCFv4.2', '##fileDate=20090805',
'##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta',
'##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">',
'##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">',
'##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001'
]
self.vcf = Vcf()
self.vcf.add_header(header_lines)
def test_bnd_alt_string(self):
self.assertEqual(self.converter.parse_bnd_alt_string('A[1:6['),
('[', '1', 6))
self.assertEqual(self.converter.parse_bnd_alt_string('A]1:6]'),
(']', '1', 6))
self.assertEqual(self.converter.parse_bnd_alt_string(']1:6]A'),
(']', '1', 6))
with self.assertRaises(AssertionError):
self.converter.parse_bnd_alt_string(']1:6[A')
with self.assertRaises(AssertionError):
self.converter.parse_bnd_alt_string('1')
def test_bnd_breakpoints(self):
vcf_array1 = [
'1', '20000', '235', 'T', 'A[1:6[', '0.00', '.', '.', 'GT', '0/0'
]
v1 = Variant(vcf_array1, self.vcf)
self.assertEqual(self.converter.bnd_breakpoints(v1),
('1', 20000, 20000, '1', 5, 5, '+', '-'))
vcf_array2 = [
'1', '20000', '235', 'T', ']1:6]N', '0.00', '.', '.', 'GT', '0/0'
]
v2 = Variant(vcf_array2, self.vcf)
self.assertEqual(self.converter.bnd_breakpoints(v2),
('1', 19999, 19999, '1', 6, 6, '-', '+'))
def test_simple_breakpoints(self):
vcf_array1 = [
'1', '20000', '235', 'T', '<DEL>', '0.00', '.', 'END=20500', 'GT',
'0/0'
]
v1 = Variant(vcf_array1, self.vcf)
self.assertEqual(self.converter.simple_breakpoints(v1),
('1', 20000, 20000, '1', 20500, 20500, '+', '-'))
vcf_array2 = [
'1', '20000', '235', 'T', '<DEL>', '0.00', '.',
'END=20500;STRANDS=-+:2', 'GT', '0/0'
]
v2 = Variant(vcf_array2, self.vcf)
self.assertEqual(self.converter.simple_breakpoints(v2),
('1', 20000, 20000, '1', 20500, 20500, '-', '+'))
vcf_array3 = [
'1', '20000', '235', 'T', '<DEL>', '0.00', '.', 'STRANDS=--:2',
'GT', '0/0'
]
v3 = Variant(vcf_array3, self.vcf)
with self.assertRaises(ValueError):
self.converter.simple_breakpoints(v3)
def test_adjust_coordinate(self):
vcf_array1 = [
'1', '20000', '235', 'T', '<DEL>', '0.00', '.', 'CIEND=-50,50',
'GT', '0/0'
]
v1 = Variant(vcf_array1, self.vcf)
self.assertEqual(
self.converter.adjust_coordinate(v1, 'CIEND', 500, 1000),
(450, 1050))
self.assertEqual(
self.converter.adjust_coordinate(v1, 'CIPOS', 500, 1000),
(500, 1000))
vcf_array2 = [
'1', '20000', '235', 'T', '<DEL>', '0.00', '.', 'CIEND=50', 'GT',
'0/0'
]
v2 = Variant(vcf_array2, self.vcf)
with self.assertRaises(ValueError):
self.converter.adjust_coordinate(v2, 'CIEND', 500, 1000)
class TestVcfToBedpeConverter(TestCase):
def setUp(self):
self.converter = VcfToBedpeConverter()
header_lines = [
'##fileformat=VCFv4.2',
'##fileDate=20090805',
'##reference=file:///seq/references/1000GenomesPilot-NCBI36.fasta',
'##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">',
'##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency">',
'##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001']
self.vcf = Vcf()
self.vcf.add_header(header_lines)
def test_bnd_alt_string(self):
self.assertEqual(self.converter.parse_bnd_alt_string('A[1:6['), ('[', '1', 6))
self.assertEqual(self.converter.parse_bnd_alt_string('A]1:6]'), (']', '1', 6))
self.assertEqual(self.converter.parse_bnd_alt_string(']1:6]A'), (']', '1', 6))
with self.assertRaises(AssertionError):
self.converter.parse_bnd_alt_string(']1:6[A')
with self.assertRaises(AssertionError):
self.converter.parse_bnd_alt_string('1')
def test_bnd_breakpoints(self):
vcf_array1 = ['1', '20000', '235', 'T', 'A[1:6[', '0.00', '.', '.', 'GT', '0/0']
v1 = Variant(vcf_array1, self.vcf)
self.assertEqual(
self.converter.bnd_breakpoints(v1),
('1', 20000, 20000, '1', 5, 5, '+', '-'))
vcf_array2 = ['1', '20000', '235', 'T', ']1:6]N', '0.00', '.', '.', 'GT', '0/0']
v2 = Variant(vcf_array2, self.vcf)
self.assertEqual(
self.converter.bnd_breakpoints(v2),
('1', 19999, 19999, '1', 6, 6, '-', '+'))
def test_simple_breakpoints(self):
vcf_array1 = ['1', '20000', '235', 'T', '<DEL>', '0.00', '.', 'END=20500', 'GT', '0/0']
v1 = Variant(vcf_array1, self.vcf)
self.assertEqual(
self.converter.simple_breakpoints(v1),
('1', 20000, 20000, '1', 20500, 20500, '+', '-'))
vcf_array2 = ['1', '20000', '235', 'T', '<DEL>', '0.00', '.', 'END=20500;STRANDS=-+:2', 'GT', '0/0']
v2 = Variant(vcf_array2, self.vcf)
self.assertEqual(
self.converter.simple_breakpoints(v2),
('1', 20000, 20000, '1', 20500, 20500, '-', '+'))
vcf_array3 = ['1', '20000', '235', 'T', '<DEL>', '0.00', '.', 'STRANDS=--:2', 'GT', '0/0']
v3 = Variant(vcf_array3, self.vcf)
with self.assertRaises(ValueError):
self.converter.simple_breakpoints(v3)
def test_adjust_coordinate(self):
vcf_array1 = ['1', '20000', '235', 'T', '<DEL>', '0.00', '.', 'CIEND=-50,50', 'GT', '0/0']
v1 = Variant(vcf_array1, self.vcf)
self.assertEqual(
self.converter.adjust_coordinate(v1, 'CIEND', 500, 1000),
(450, 1050))
self.assertEqual(
self.converter.adjust_coordinate(v1, 'CIPOS', 500, 1000),
(500, 1000))
vcf_array2 = ['1', '20000', '235', 'T', '<DEL>', '0.00', '.', 'CIEND=50', 'GT', '0/0']
v2 = Variant(vcf_array2, self.vcf)
with self.assertRaises(ValueError):
self.converter.adjust_coordinate(v2, 'CIEND', 500, 1000)
