Python Bedpe.retrieve_svtype Examples

Example #1

File: bedpe_tests.py Project: hall-lab/svtools

 def test_retrieve_svtype(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(b1.retrieve_svtype(), 'BND')
     entry2 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'AF=0.2', 'AF=0.2' ]
     with self.assertRaises(SystemExit):
         b = Bedpe(entry2)
     entry3 = [ '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-', 'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'SVTYPE=BND;AF=0.2;ORIG_SVTYPE=DEL', 'SVTYPE=BND;AF=0.2;ORIG_SVTYPE=DEL' ]
     b3 = Bedpe(entry3)
     self.assertEqual(b3.retrieve_svtype(), 'BND')

Example #2

File: bedpe_tests.py Project: zyworship/svtools

 def test_retrieve_svtype(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(b1.retrieve_svtype(), 'BND')
     entry2 = [
         '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
         'BND', 'PASS', '.', '.', '.', '.', '.', '.', 'AF=0.2', 'AF=0.2'
     ]
     with self.assertRaises(SystemExit):
         b = Bedpe(entry2)
     entry3 = [
         '1', '200', '300', '2', '300', '400', '777_1', '57', '+', '-',
         'BND', 'PASS', '.', '.', '.', '.', '.', '.',
         'SVTYPE=BND;AF=0.2;ORIG_SVTYPE=DEL',
         'SVTYPE=BND;AF=0.2;ORIG_SVTYPE=DEL'
     ]
     b3 = Bedpe(entry3)
     self.assertEqual(b3.retrieve_svtype(), 'BND')