class TestVariant(TestCase):
def setUp(self):
header_lines = [
'##fileformat=VCFv4.2',
'##fileDate=20151202',
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
'#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878' ]
self.vcf = Vcf()
self.vcf.add_header(header_lines)
self.variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU 0/0:9'
self.variant = Variant(self.variant_line.split('\t'), self.vcf)
def test_set_info(self):
self.variant.set_info('SVTYPE', 'INV')
self.assertEqual(self.variant.info['SVTYPE'], 'INV')
self.variant.set_info('IMAFLAG', False)
self.assertEqual(self.variant.info['IMAFLAG'], False)
with self.assertRaises(SystemExit) as cm:
self.variant.set_info('SUPER', True)
def test_get_info(self):
self.assertEqual(self.variant.get_info('IMAFLAG'), True)
self.assertEqual(self.variant.get_info('SVTYPE'), 'BND')
with self.assertRaises(KeyError) as cm:
self.variant.get_info('CALI')
def test_get_info_string(self):
self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9;IMAFLAG')
self.variant.set_info('IMAFLAG', False)
self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9')
def test_get_format_string(self):
self.assertEqual(self.variant.get_format_string(), 'GT:SU')
def test_genotype(self):
self.assertEqual(self.variant.genotype('NA12878').get_gt_string(), '0/0:9')
def test_var_string(self):
self.assertEqual(self.variant.get_var_string(), self.variant_line)
class TestVariant(TestCase):
def setUp(self):
header_lines = [
'##fileformat=VCFv4.2', '##fileDate=20151202',
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
'#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA0001'
]
self.vcf = Vcf()
self.vcf.add_header(header_lines)
self.variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU 0/0:9 1/1:15'
self.variant = Variant(self.variant_line.split('\t'), self.vcf)
def test_parse_genotypes(self):
genotype_field_strings = ['0/1:20', '0/0:15']
parsed_dict = self.variant._parse_genotypes(genotype_field_strings)
na12878_gt = Genotype(self.variant,
genotype_field_strings[0].split(':'))
na0001_gt = Genotype(self.variant,
genotype_field_strings[1].split(':'))
expected_genotype_dict = {'NA12878': na12878_gt, 'NA0001': na0001_gt}
self.assertEqual(parsed_dict, expected_genotype_dict)
def test_set_info(self):
self.variant.set_info('SVTYPE', 'INV')
self.assertEqual(self.variant.info['SVTYPE'], 'INV')
self.variant.set_info('IMAFLAG', False)
self.assertEqual(self.variant.info['IMAFLAG'], False)
with self.assertRaises(SystemExit) as cm:
self.variant.set_info('SUPER', True)
def test_get_info(self):
self.assertEqual(self.variant.get_info('IMAFLAG'), True)
self.assertEqual(self.variant.get_info('SVTYPE'), 'BND')
with self.assertRaises(KeyError) as cm:
self.variant.get_info('CALI')
def test_get_info_string(self):
self.assertEqual(self.variant.get_info_string(),
'SVTYPE=BND;STRANDS=-+:9;IMAFLAG')
self.variant.set_info('IMAFLAG', False)
self.assertEqual(self.variant.get_info_string(),
'SVTYPE=BND;STRANDS=-+:9')
def test_get_format_string(self):
self.assertEqual(self.variant.get_format_string(), 'GT:SU')
def test_get_gt_string(self):
self.assertEqual(self.variant.get_gt_string(), '0/0:9 1/1:15')
def test_genotype(self):
self.assertEqual(
self.variant.genotype('NA12878').get_gt_string(), '0/0:9')
def test_genotypes(self):
self.assertEqual([x.get_gt_string() for x in self.variant.genotypes()],
['0/0:9', '1/1:15'])
def test_var_string(self):
self.assertEqual(self.variant.get_var_string(), self.variant_line)
self.variant.genotype('NA12878').set_format('GT', './.')
self.assertEqual(
self.variant.get_var_string(use_cached_gt_string=True),
self.variant_line)
self.assertNotEqual(self.variant.get_var_string(), self.variant_line)
class TestVariant(TestCase):
def setUp(self):
header_lines = [
"##fileformat=VCFv4.2",
"##fileDate=20151202",
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA0001",
]
self.vcf = Vcf()
self.vcf.add_header(header_lines)
self.variant_line = (
"1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU 0/0:9 1/1:15"
)
self.variant = Variant(self.variant_line.split("\t"), self.vcf)
def test_parse_genotypes(self):
genotype_field_strings = ["0/1:20", "0/0:15"]
parsed_dict = self.variant._parse_genotypes(genotype_field_strings)
na12878_gt = Genotype(self.variant, genotype_field_strings[0].split(":"))
na0001_gt = Genotype(self.variant, genotype_field_strings[1].split(":"))
expected_genotype_dict = {"NA12878": na12878_gt, "NA0001": na0001_gt}
self.assertEqual(parsed_dict, expected_genotype_dict)
def test_set_info(self):
self.variant.set_info("SVTYPE", "INV")
self.assertEqual(self.variant.info["SVTYPE"], "INV")
self.variant.set_info("IMAFLAG", False)
self.assertEqual(self.variant.info["IMAFLAG"], False)
with self.assertRaises(SystemExit) as cm:
self.variant.set_info("SUPER", True)
def test_get_info(self):
self.assertEqual(self.variant.get_info("IMAFLAG"), True)
self.assertEqual(self.variant.get_info("SVTYPE"), "BND")
with self.assertRaises(KeyError) as cm:
self.variant.get_info("CALI")
def test_get_info_string(self):
self.assertEqual(self.variant.get_info_string(), "SVTYPE=BND;STRANDS=-+:9;IMAFLAG")
self.variant.set_info("IMAFLAG", False)
self.assertEqual(self.variant.get_info_string(), "SVTYPE=BND;STRANDS=-+:9")
def test_get_format_string(self):
self.assertEqual(self.variant.get_format_string(), "GT:SU")
def test_get_format_string_caching(self):
header_lines = [
"##fileformat=VCFv4.2",
"##fileDate=20151202",
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=AS,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878",
]
vcf = Vcf()
vcf.add_header(header_lines)
variant_line = "1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:AS:SU 0/0:1:9"
variant = Variant(variant_line.split("\t"), vcf)
self.assertEqual(variant.get_format_string(), "GT:AS:SU")
gts = variant.genotypes()
self.assertEqual(variant.get_format_string(), "GT:SU:AS")
self.assertEqual(variant.get_format_string(True), "GT:AS:SU")
def test_get_gt_string(self):
self.assertEqual(self.variant.get_gt_string(), "0/0:9 1/1:15")
def test_genotype(self):
self.assertEqual(self.variant.genotype("NA12878").get_gt_string(), "0/0:9")
def test_set_genotype(self):
new_genotype = Genotype(self.variant, ["0/1", "9"])
self.variant.set_genotype("NA12878", new_genotype)
self.assertEqual(self.variant.genotype("NA12878").get_gt_string(), "0/1:9")
def test_genotypes(self):
self.assertEqual([x.get_gt_string() for x in self.variant.genotypes()], ["0/0:9", "1/1:15"])
def test_var_string(self):
self.assertEqual(self.variant.get_var_string(), self.variant_line)
self.variant.genotype("NA12878").set_format("GT", "./.")
self.assertEqual(self.variant.get_var_string(use_cached_gt_string=True), self.variant_line)
self.assertNotEqual(self.variant.get_var_string(), self.variant_line)
def test_var_string_format_caching(self):
header_lines = [
"##fileformat=VCFv4.2",
"##fileDate=20151202",
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=AS,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878",
]
vcf = Vcf()
vcf.add_header(header_lines)
variant_line = "1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:AS:SU 0/0:1:9"
uncached_line = "1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU:AS 0/0:9:1"
variant = Variant(variant_line.split("\t"), vcf)
gt = variant.genotypes() # force parsing
self.assertEqual(variant.get_var_string(), uncached_line)
self.assertEqual(variant.get_var_string(use_cached_gt_string=True), variant_line)
def test_add_genotype(self):
header_lines = [
"##fileformat=VCFv4.2",
"##fileDate=20151202",
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
"#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878",
]
vcf = Vcf()
vcf.add_header(header_lines)
variant_line = "1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG SU 9"
variant = Variant(variant_line.split("\t"), vcf)
self.assertEqual(variant.get_gt_string(), "./.:9")
class TestVariant(TestCase):
def setUp(self):
header_lines = [
'##fileformat=VCFv4.2',
'##fileDate=20151202',
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
'#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 NA0001' ]
self.vcf = Vcf()
self.vcf.add_header(header_lines)
self.variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG GT:SU 0/0:9 1/1:15'
self.variant = Variant(self.variant_line.split('\t'), self.vcf)
def test_parse_genotypes(self):
genotype_field_strings = ['0/1:20', '0/0:15']
parsed_dict = self.variant._parse_genotypes(genotype_field_strings)
na12878_gt = Genotype(self.variant, genotype_field_strings[0].split(':'))
na0001_gt = Genotype(self.variant, genotype_field_strings[1].split(':'))
expected_genotype_dict = { 'NA12878': na12878_gt, 'NA0001': na0001_gt }
self.assertEqual(parsed_dict, expected_genotype_dict)
def test_set_info(self):
self.variant.set_info('SVTYPE', 'INV')
self.assertEqual(self.variant.info['SVTYPE'], 'INV')
self.variant.set_info('IMAFLAG', False)
self.assertEqual(self.variant.info['IMAFLAG'], False)
with self.assertRaises(SystemExit) as cm:
self.variant.set_info('SUPER', True)
def test_get_info(self):
self.assertEqual(self.variant.get_info('IMAFLAG'), True)
self.assertEqual(self.variant.get_info('SVTYPE'), 'BND')
with self.assertRaises(KeyError) as cm:
self.variant.get_info('CALI')
def test_get_info_string(self):
self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9;IMAFLAG')
self.variant.set_info('IMAFLAG', False)
self.assertEqual(self.variant.get_info_string(), 'SVTYPE=BND;STRANDS=-+:9')
def test_get_format_string(self):
self.assertEqual(self.variant.get_format_string(), 'GT:SU')
def test_get_gt_string(self):
self.assertEqual(self.variant.get_gt_string(), '0/0:9 1/1:15')
def test_genotype(self):
self.assertEqual(self.variant.genotype('NA12878').get_gt_string(), '0/0:9')
def test_genotypes(self):
self.assertEqual([ x.get_gt_string() for x in self.variant.genotypes() ], ['0/0:9', '1/1:15'])
def test_var_string(self):
self.assertEqual(self.variant.get_var_string(), self.variant_line)
self.variant.genotype('NA12878').set_format('GT', './.')
self.assertEqual(self.variant.get_var_string(use_cached_gt_string=True), self.variant_line)
self.assertNotEqual(self.variant.get_var_string(), self.variant_line)
def test_add_genotype(self):
header_lines = [
'##fileformat=VCFv4.2',
'##fileDate=20151202',
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
'#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878' ]
vcf = Vcf()
vcf.add_header(header_lines)
variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG SU 9'
variant = Variant(variant_line.split('\t'), vcf)
self.assertEqual(variant.get_gt_string(), './.:9')
class TestVariant8Col(TestCase):
def setUp(self):
header_lines = [
'##fileformat=VCFv4.2', '##fileDate=20151202',
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
'#CHROM POS ID REF ALT QUAL FILTER INFO'
]
self.vcf = Vcf()
self.vcf.add_header(header_lines)
self.variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG'
self.variant = Variant(self.variant_line.split('\t'), self.vcf)
def test_set_info(self):
self.variant.set_info('SVTYPE', 'INV')
self.assertEqual(self.variant.info['SVTYPE'], 'INV')
self.variant.set_info('IMAFLAG', False)
self.assertEqual(self.variant.info['IMAFLAG'], False)
with self.assertRaises(SystemExit) as cm:
self.variant.set_info('SUPER', True)
def test_get_info(self):
self.assertEqual(self.variant.get_info('IMAFLAG'), True)
self.assertEqual(self.variant.get_info('SVTYPE'), 'BND')
with self.assertRaises(KeyError) as cm:
self.variant.get_info('CALI')
def test_get_info_string(self):
self.assertEqual(self.variant.get_info_string(),
'SVTYPE=BND;STRANDS=-+:9;IMAFLAG')
self.variant.set_info('IMAFLAG', False)
self.assertEqual(self.variant.get_info_string(),
'SVTYPE=BND;STRANDS=-+:9')
def test_get_format_string(self):
self.assertEqual(self.variant.get_format_string(), None)
def test_get_format_string_caching(self):
header_lines = [
'##fileformat=VCFv4.2', '##fileDate=20151202',
'##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">',
'##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">',
'##INFO=<ID=IMAFLAG,Number=.,Type=Flag,Description="Test Flag code">',
'##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">',
'##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=AS,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">',
'##FORMAT=<ID=INACTIVE,Number=1,Type=Integer,Description="A format not in use">',
'#CHROM POS ID REF ALT QUAL FILTER INFO'
]
vcf = Vcf()
vcf.add_header(header_lines)
variant_line = '1 820915 5838_1 N ]GL000232.1:20940]N 0.00 . SVTYPE=BND;STRANDS=-+:9;IMAFLAG'
variant = Variant(variant_line.split('\t'), vcf)
self.assertEqual(variant.get_format_string(), None)
gts = variant.genotypes()
self.assertEqual(variant.get_format_string(), None)
self.assertEqual(variant.get_format_string(True), None)
def test_get_gt_string(self):
self.assertEqual(self.variant.get_gt_string(), None)
def test_genotypes(self):
self.assertEqual(self.variant.genotypes(), [])
def test_var_string(self):
self.assertEqual(self.variant.get_var_string(), self.variant_line)
