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_add_header(self):
contig = EMBLContig()
contig.features['feature_1'] = self.create_blank_bit_of_contig()
contig.sequence = self.create_blank_bit_of_contig()
header_details = {
"authors": "John Doe",
"classification": "UNC",
"genome_type": "circular",
"organism": "My organism",
"project": "PRJ1234",
"publication": "Unpublished",
"sequence_identifier": "**contig123",
"sequence_length": 8,
"sequence_name": "chromX",
"taxon_id": 5678,
"title": "My title"
}
contig.add_header(**header_details)
self.assertIsInstance(contig.header, EMBLHeader)
with self.assertRaises(ValueError):
contig.add_header(**header_details)
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)
def test_format_no_header(self): contig = EMBLContig() contig.features['feature_1'] = self.create_blank_bit_of_contig() contig.sequence = self.create_blank_bit_of_contig() self.assertEqual(contig.header, None) self.assertRaises(ValueError, contig.format)
def test_format_no_features(self): contig = EMBLContig() contig.header = self.create_blank_bit_of_contig() contig.sequence = self.create_blank_bit_of_contig() self.assertEquals(contig.format(), '')
