def test_find_overlaps():
r1 = Range(start=np.array([1, 4, 8]), end=np.array([2, 7, 10]))
q1 = Range(start=np.array([3]), end=np.array([5]))
fo = FindOverlaps(subject=r1)
assert fo.index == NCList(None, [NCList(0), NCList(1), NCList(2)])
for x in fo.query(query=q1):
pass
overlapped = list(fo.query(query=q1))
assert len(overlapped) == 1
assert overlapped == [Range(start=np.array([4]), end=np.array([7]))]
def test_search_in_builded_nc_list():
# 0 0->1 0->0 0 1 1 1
# 0 1 2 3 4 5 6
a = [False, True, True, False, True, True, False]
nc = NCList(None, [
NCList(0),
NCList(1, [NCList(4), NCList(5), NCList(6)]),
NCList(2),
NCList(3)
])
assert list(nc.find_overlap_index(lambda i: a[i])) == [1, 2, 4, 5]
def test_building_nclist_on_sorted_data(interval_arrays1):
s, e, idx = interval_arrays1
ncb = NCListBuilder(Intervals(s, e))
ncb.index = idx
assert (ncb._construct_nclist_from_sorted_index() == NCList(
None, [NCList(4, [NCList(0), NCList(1)]),
NCList(3, [NCList(2)])]))
def test_nc_list_child_interfaces():
assert NCList(None).childs() == 0
def test_counting_nc_list_on_modification_and_creation():
ncl = NCList(None)
ncl.append(NCList(1))
assert len(ncl.childs) == 1
assert len(ncl) == 1
assert len(NCList(None, [NCList(1, [NCList(2)])])) == 2
def test_nc_list_equality():
assert NCList(1) == NCList(1)
assert NCList(1) != NCList(2)
assert NCList(1, [NCList(2)]) != NCList(1, [NCList(3)])
assert NCList(1, [NCList(2, [NCList(3)])]) != NCList(
1, [NCList(2, [NCList(4)])])
def test_nonempty_nclist():
ncl = NCList(None, [NCList(1), NCList(2), NCList(3)])
assert list(ncl) == [1, 2, 3]
def test_empty_nclist():
NCList(0)
def test_nclist_repr():
assert NCList(None, []).__repr__() == 'NCList(None)'
assert (NCList(
None,
[NCList(0, [NCList(1), NCList(2)])
]).__repr__() == 'NCList(None, [NCList(0, [NCList(1), NCList(2)])])')