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)
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')
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)