def test_format_line_too_long(self):
contig = EMBLContig()
header_mock = MagicMock()
sequence_mock = MagicMock()
header_mock.format.return_value = "Header"
sequence_mock.format.return_value = "Very long line: " + '*'*100
contig.header = header_mock
contig.features = {}
contig.sequence = sequence_mock
self.assertRaises(ValueError, contig.format)
def test_get_sorted_features_3(self):
# Must be able to get a list of features sorted by (start, end) irrespective of strand
contig = EMBLContig()
feature_1 = MagicMock()
feature_1.start = 100
feature_1.end = 1500
feature_2 = MagicMock()
feature_2.start = 1100
feature_2.end = 2000
contig.features = {1: feature_1, 2: feature_2}
expected_features = [feature_1, feature_2]
self.assertEquals(contig.sorted_features(), expected_features)
contig.features = {2: feature_2, 1: feature_1}
expected_features = [feature_1, feature_2]
self.assertEquals(contig.sorted_features(), expected_features)
contig.features = {2: feature_1, 1: feature_2}
expected_features = [feature_1, feature_2]
self.assertEquals(contig.sorted_features(), expected_features)
def test_format(self):
contig = EMBLContig()
header_mock = MagicMock()
feature_mock_1 = MagicMock()
feature_mock_2 = MagicMock()
sequence_mock = MagicMock()
header_mock.format.return_value = "Header\n"
feature_mock_1.format.return_value = "Feature 1\n"
feature_mock_1.start = 0
feature_mock_2.format.return_value = "Feature 2\n"
feature_mock_2.start = 100
sequence_mock.format.return_value = "Sequence\n"
contig.header = header_mock
contig.features = {1: feature_mock_1, 2: feature_mock_2}
contig.sequence = sequence_mock
calculated_string = contig.format()
expected_string = """\
Header
Feature 1
Feature 2
Sequence
"""
self.assertEqual(calculated_string, expected_string)
