def test_parse_loc_str_invalid(self): length = 12 examples = ['abc', '3-8'] for example in examples: with six.assertRaisesRegex( self, GenBankFormatError, 'Could not parse location string: ' '"%s"' % example): _parse_loc_str(example, length)
def test_parse_loc_str_invalid(self): length = 12 examples = [ 'abc', '3-8'] for example in examples: with self.assertRaisesRegex(GenBankFormatError, 'Could not parse location string: ' '"%s"' % example): _parse_loc_str(example, length)
def test_parse_loc_str(self): length = 12 examples = [ "", "9", # a single base in the presented sequence "3..8", "<3..8", "1..>8", "complement(3..8)", "complement(join(3..5,7..9))", "join(3..5,7..9)", "J00194.1:1..9", "1.9", "1^9", ] expects = [ ( {"right_partial_": False, "left_partial_": False, "rc_": False}, np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype=bool), ), ( {"right_partial_": False, "left_partial_": False, "rc_": False}, np.array([0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], dtype=bool), ), ( {"right_partial_": False, "left_partial_": False, "rc_": False}, np.array([0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0], dtype=bool), ), ( {"right_partial_": False, "left_partial_": True, "rc_": False}, np.array([0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0], dtype=bool), ), ( {"right_partial_": True, "left_partial_": False, "rc_": False}, np.array([1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0], dtype=bool), ), ( {"right_partial_": False, "left_partial_": False, "rc_": True}, np.array([0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0], dtype=bool), ), ( {"right_partial_": False, "left_partial_": False, "rc_": True}, np.array([0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0], dtype=bool), ), ( {"right_partial_": False, "left_partial_": False, "rc_": False}, np.array([0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0], dtype=bool), ), ({"right_partial_": False, "left_partial_": False, "rc_": False}, np.zeros(length, dtype=bool)), ({"right_partial_": False, "left_partial_": False, "rc_": False}, np.zeros(length, dtype=bool)), ({"right_partial_": False, "left_partial_": False, "rc_": False}, np.zeros(length, dtype=bool)), ] for example, expect in zip(examples, expects): parsed = _parse_loc_str(example, length) self.assertDictEqual(parsed[0], expect[0]) npt.assert_equal(parsed[1], expect[1])
def test_parse_loc_str(self): length = 12 examples = [ '', '9', # a single base in the presented sequence '3..8', '<3..8', '1..>8', 'complement(3..8)', 'complement(join(3..5,7..9))', 'join(3..5,7..9)', 'J00194.1:1..9', '1.9', '1^9'] expects = [ ({'right_partial_': False, 'left_partial_': False, 'rc_': False}, np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0], dtype=bool)), ({'right_partial_': False, 'left_partial_': False, 'rc_': False}, np.array([0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0], dtype=bool)), ({'right_partial_': False, 'left_partial_': False, 'rc_': False}, np.array([0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0], dtype=bool)), ({'right_partial_': False, 'left_partial_': True, 'rc_': False}, np.array([0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0], dtype=bool)), ({'right_partial_': True, 'left_partial_': False, 'rc_': False}, np.array([1, 1, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0], dtype=bool)), ({'right_partial_': False, 'left_partial_': False, 'rc_': True}, np.array([0, 0, 1, 1, 1, 1, 1, 1, 0, 0, 0, 0], dtype=bool)), ({'right_partial_': False, 'left_partial_': False, 'rc_': True}, np.array([0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0], dtype=bool)), ({'right_partial_': False, 'left_partial_': False, 'rc_': False}, np.array([0, 0, 1, 1, 1, 0, 1, 1, 1, 0, 0, 0], dtype=bool)), ({'right_partial_': False, 'left_partial_': False, 'rc_': False}, np.zeros(length, dtype=bool)), ({'right_partial_': False, 'left_partial_': False, 'rc_': False}, np.zeros(length, dtype=bool)), ({'right_partial_': False, 'left_partial_': False, 'rc_': False}, np.zeros(length, dtype=bool))] for example, expect in zip(examples, expects): parsed = _parse_loc_str(example, length) self.assertDictEqual(parsed[0], expect[0]) npt.assert_equal(parsed[1], expect[1])
def test_parse_loc_str_invalid(self): length = 12 examples = ["abc", "3-8"] for example in examples: with six.assertRaisesRegex(self, GenBankFormatError, "Could not parse location string: " '"%s"' % example): _parse_loc_str(example, length)