def setUp(self):
self.feature = tmrna.Tmrna()
self.seq1 = Seq("AATTCGAGCT")
self.seqfeature1 = test_data_utils.create_1_part_seqfeature(
1, 5, 1, "CDS")
self.seqfeature2 = test_data_utils.create_1_part_seqfeature(
1, 5, -1, "CDS")
self.seqfeature3 = test_data_utils.create_2_part_seqfeature(
1, 5, 1, 3, 7, 1, "CDS")
def test_parse_coordinates_6(self):
"""Verify undefined strand 2-part compound location is not parsed."""
seqfeature = test_data_utils.create_2_part_seqfeature(
2, 10, None, 8, 20, None, "CDS")
start, stop, parts = flat_files.parse_coordinates(seqfeature)
with self.subTest():
self.assertEqual(start, -1)
with self.subTest():
self.assertEqual(stop, -1)
with self.subTest():
self.assertEqual(parts, 0)
def test_parse_coordinates_3(self):
"""Verify -1 strand 2-part compound location is parsed correctly."""
seqfeature = test_data_utils.create_2_part_seqfeature(
2, 10, -1, 8, 20, -1, "CDS")
start, stop, parts = flat_files.parse_coordinates(seqfeature)
with self.subTest():
self.assertEqual(start, 8)
with self.subTest():
self.assertEqual(stop, 10)
with self.subTest():
self.assertEqual(parts, 2)