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)