def test_parse_coordinates_8(self):
"""Verify location of invalid data type is not parsed."""
seqfeature = SeqFeature(None, type="CDS", strand=None)
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_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)
def test_parse_coordinates_7(self):
"""Verify 1 strand 3-part compound location is not parsed."""
seqfeature = test_data_utils.create_3_part_seqfeature(
2, 10, 1, 8, 20, 1, 30, 50, 1, "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, 3)
def test_parse_coordinates_1(self):
"""Verify non-compound location is parsed correctly."""
seqfeature = test_data_utils.create_1_part_seqfeature(2, 10, 1, "CDS")
output_start, output_stop, parts = \
flat_files.parse_coordinates(seqfeature)
with self.subTest():
self.assertEqual(output_start, 2)
with self.subTest():
self.assertEqual(output_stop, 10)
with self.subTest():
self.assertEqual(parts, 1)
def test_parse_coordinates_5(self):
"""Verify -1 strand 2-part compound location that wraps around
genome end is parsed correctly."""
# Wrap-around feature, directly copied from
# Biopython-parsed Lifes_Draft flat file.
# start1 = 0, stop1 = 9, start2 = 58743, stop2 = 59253, strand = -1
seqfeature = test_data_utils.get_lifes_cds_122_seqfeature()
start, stop, parts = flat_files.parse_coordinates(seqfeature)
with self.subTest():
self.assertEqual(start, 58743)
with self.subTest():
self.assertEqual(stop, 9)
with self.subTest():
self.assertEqual(parts, 2)
def test_parse_coordinates_4(self):
"""Verify 1 strand 2-part compound location that wraps around
genome end is parsed correctly."""
# Wrap-around feature, directly copied from
# Biopython-parsed Alice flat file.
# start1 = 152829, stop1 = 153401, start2 = 0, stop2 = 4, strand = 1
seqfeature = test_data_utils.get_alice_cds_252_seqfeature()
start, stop, parts = flat_files.parse_coordinates(seqfeature)
with self.subTest():
self.assertEqual(start, 152829)
with self.subTest():
self.assertEqual(stop, 4)
with self.subTest():
self.assertEqual(parts, 2)
def test_parse_coordinates_10(self):
"""Verify non-compound location with fuzzy stop coordinate
is parsed correctly."""
seqfeature = test_data_utils.create_1_part_seqfeature(2,
10,
1,
"CDS",
fuzzy="stop")
start, stop, parts = flat_files.parse_coordinates(seqfeature)
with self.subTest():
self.assertEqual(start, 2)
with self.subTest():
self.assertEqual(stop, -1)
with self.subTest():
self.assertEqual(parts, 1)