def test_alternate_orderings(self):
loc = build_compound([(0, 3), (6, 9), (12, 15)], -1)
assert loc.parts[0].start == 0
assert is_bridged(loc)
assert loc.parts[0].start == 0
assert not is_bridged(loc, allow_reversing=True)
assert loc.parts[0].start == 12
loc = build_compound([(12, 15), (6, 9), (0, 3)], -1)
assert loc.parts[0].start == 12
assert not is_bridged(loc, allow_reversing=True)
assert loc.parts[0].start == 12
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_indeterminate(self):
assert is_bridged(build_compound([(0, 3), (12, 15), (6, 9)], -1),
allow_reversing=True)
def test_not_bridged(self):
assert not is_bridged(build_compound([(1, 6), (5, 10)], 1))
assert not is_bridged(build_compound([(5, 10), (1, 6)], -1))
def test_bad_strand(self):
pairs = [(9, 12), (0, 3)]
assert is_bridged(build_compound(pairs, 1))
assert not is_bridged(build_compound(pairs, None))
def test_reverse(self):
assert is_bridged(build_compound([(0, 3), (9, 12)], -1))
assert is_bridged(build_compound([(6, 9), (0, 3), (15, 18)], -1))
assert is_bridged(build_compound([(0, 3), (15, 18), (6, 9)], -1))
assert not is_bridged(build_compound([(9, 12), (0, 3)], -1))
def test_forward(self):
assert is_bridged(build_compound([(9, 12), (0, 3)], 1))
assert is_bridged(build_compound([(9, 12), (0, 3), (4, 5)], 1))
assert is_bridged(build_compound([(4, 5), (9, 12), (0, 3)], 1))
assert not is_bridged(build_compound([(0, 3), (9, 12)], 1))