Python Bedpe.parse_info_tag Examples

Example #1

 def test_parse_info_tag(self):
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE', 'SVTYPE'), True)
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE', 'AF='), False)
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;AF=0.2', 'AF='),
                      '0.2')
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;AF=0.2', 'SVTYPE='),
                      'BND')
     self.assertEqual(
         Bedpe.parse_info_tag('SVTYPE=BND;SECONDARY;AF=0.2', 'SECONDARY'),
         True)

Example #2

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

 def test_parse_info_tag(self):
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE', 'SVTYPE'), True)
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE', 'AF='), False)
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;AF=0.2', 'AF='), '0.2')
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;AF=0.2', 'SVTYPE='), 'BND')
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;SECONDARY;AF=0.2', 'SECONDARY'), True)
     self.assertEqual(Bedpe.parse_info_tag('SVTYPE=BND;SECONDARY;BAD_AF=0.3;AF=0.2', 'AF='), '0.2')

Example #3

File: cluster.py Project: cc2qe/svtools

 def flag_as_pruned(bedpe):
     '''
     Mark a BEDPE info field(s) as RETAINED
     '''
     if not Bedpe.parse_info_tag(bedpe.info, 'RETAINED'):
         bedpe.set_info('RETAINED', None)

Example #4

File: cluster.py Project: zyworship/svtools

 def flag_as_pruned(bedpe):
     '''
     Mark a BEDPE info field(s) as RETAINED
     '''
     if not Bedpe.parse_info_tag(bedpe.info, 'RETAINED'):
         bedpe.set_info('RETAINED', None)