class ContigsWrapperTestCase(unittest.TestCase):
def setUp(self):
self.case = ContigsWrapper("ANVW00000000", "ANVW01000000")
def tearDown(self):
del self.case
def test_add_contigs(self):
contigs = [('ANVW01000001', 'ACTGATGGCTGATCGTACGGATTGGCATCGTACTATCGATCAGCTGAGCTACG'),
('ANVW01000002', 'TTTCGAGCTGGACTGATGGCATCGGCAGGACGAGCTTCAGCTACGATCGAAA'),
('ANVW01000003', 'CCTAAGCTGGGATCGATTGAGCTAGCATTGACACACCACACCCATTTTTGT'),
('ANVW01000004', 'GAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTTTCCATTTTTACTACTAGC')]
self.case.add_contigs(contigs)
self.assertEqual(self.case.contigs, contigs)
self.assertEqual(self.case.numcontigs, 4)
self.assertEqual(self.case.basepairs, 208)
self.assertIsNotNone(self.case.checksum)
def test_generate_checksum(self):
self.case.contigs = [("a", "atcg"), ("b", "t"), ("c", "actgatgtg")]
self.case.generate_checksum()
result = "517e0a5acb941ce868da1e285a8c1372"
self.assertEqual(self.case.checksum,result)
def test_generate_kwargs(self):
with self.assertRaises(TypeError):
self.case.generate_kwargs()
sequences = [("a", "atcg"), ("b", "t"), ("c", "actgatgtg")]
self.case.add_contigs(sequences)
self.case.dict["is_from"] = "CORE"
results = {"name":"ANVW01000001",
"genome":"ANVW00000000",
"sequence":"actactactact",
"is_from":"CORE"}
self.assertEqual(self.case.generate_kwargs("ANVW01000001", "actactactact"), results)
def setUp(self):
self.case = ContigsWrapper("ANVW00000000", "ANVW01000000")