def test_extras_reverse(self):
loc = build_compound([(6, 9), (0, 3), (15, 18)], -1)
lower, upper = splitter(loc)
self.check_pairs(lower, [(6, 9), (0, 3)])
self.check_pairs(upper, [(15, 18)])
loc = build_compound([(0, 3), (15, 18), (6, 9)], -1)
lower, upper = splitter(loc)
self.check_pairs(lower, [(0, 3)])
self.check_pairs(upper, [(15, 18), (6, 9)])
def test_not_bridging_reverse(self):
loc = build_compound([(9, 12), (0, 3)], -1)
with self.assertRaisesRegex(ValueError,
"Location does not bridge origin"):
print(splitter(loc))
loc = build_compound([(15, 18), (9, 12), (0, 3)], -1)
with self.assertRaisesRegex(ValueError,
"Location does not bridge origin"):
print(splitter(loc))
def test_bad_strand(self):
loc = build_compound([(9, 12), (0, 3)], -1)
loc.parts[0].strand = 1
loc.parts[1].strand = -1
assert loc.strand is None
with self.assertRaisesRegex(ValueError, "Cannot separate bridged location without a valid strand"):
print(splitter(loc))
def test_unusable(self):
# this format crosses the origin multiple times and can't be interpreted
raw_loc_parts = [(0, 3), (6, 9), (12, 15), (18, 21)]
# test a variety of badly ordered parts
for ordering in [[0, 2, 1, 3], [0, 1, 3, 2], [0, 3, 1, 2]]:
# cycle them around to test position independence
for i in range(len(ordering)):
loc_parts = [
raw_loc_parts[i] for i in ordering[i:] + ordering[:i]
]
# forward
loc = build_compound(loc_parts, 1)
assert is_bridged(loc)
with self.assertRaisesRegex(
ValueError, "cannot determine correct ordering"):
splitter(loc)
# reverse
loc = build_compound(loc_parts[::-1], -1)
assert is_bridged(loc)
with self.assertRaisesRegex(
ValueError, "cannot determine correct ordering"):
splitter(loc)
def test_frameshifts(self):
loc = build_compound([(4772224, 4772573), (4772572, 4773186),
(0, 258)], 1)
low, high = splitter(loc)
assert low == loc.parts[2:]
assert high == loc.parts[0:2]
def test_not_bridging_forward(self):
loc = build_compound([(0, 3), (9, 12)], 1)
with self.assertRaisesRegex(ValueError,
"Location does not bridge origin"):
print(splitter(loc))
def test_simple_reverse(self):
loc = build_compound([(0, 3), (9, 12)], -1)
lower, upper = splitter(loc)
self.check_pairs(lower, [(0, 3)])
self.check_pairs(upper, [(9, 12)])
def test_simple_forward(self):
loc = build_compound([(9, 12), (0, 3)], 1)
lower, upper = splitter(loc)
self.check_pairs(lower, [(0, 3)])
self.check_pairs(upper, [(9, 12)])
