class TestBedpeToVcfConverter(TestCase):
def setUp(self):
vcf = Vcf()
self.converter = BedpeToVcfConverter(vcf)
def test_adjust_by_cipos(self):
entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
b1 = Bedpe(entry1)
self.assertEqual(self.converter.adjust_by_cipos(b1), 200)
b1.o1 = '-'
self.assertEqual(self.converter.adjust_by_cipos(b1), 201)
b1.info1 = 'SVTYPE=BND;AF=0.2;CIPOS=-2,3'
self.assertEqual(self.converter.adjust_by_cipos(b1), 203)
b1.o1 = '+'
self.assertEqual(self.converter.adjust_by_cipos(b1), 202)
def test_adjust_by_ciend(self):
entry1 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', 'SVTYPE=BND;AF=0.2', 'SVTYPE=BND;AF=0.2' ]
b1 = Bedpe(entry1)
self.assertEqual(self.converter.adjust_by_ciend(b1), 301)
b1.o2 = '+'
self.assertEqual(self.converter.adjust_by_ciend(b1), 300)
b1.info1 = 'SVTYPE=BND;AF=0.2;CIEND=-2,3'
self.assertEqual(self.converter.adjust_by_ciend(b1), 302)
b1.o2 = '-'
self.assertEqual(self.converter.adjust_by_ciend(b1), 303)
def test_determine_sep(self):
self.assertEqual(self.converter.determine_sep('-'), '[')
self.assertEqual(self.converter.determine_sep('+'), ']')
def test_determine_flanks(self):
self.assertEqual(self.converter.determine_flanks('-'), ('', 'N'))
self.assertEqual(self.converter.determine_flanks('+'), ('N', ''))
def test_bnd_alt_string(self):
self.assertEqual(self.converter.bnd_alt_string('+', '-', '2', '22222'), 'N[2:22222[')
self.assertEqual(self.converter.bnd_alt_string('-', '+', '2', '22222'), ']2:22222]N')
