def test_region_properties():
# Properties of linear region
r = Region(1, 5, context=Context(10, False, start_index=1))
assert r.start == 1
assert r.end == 5
assert r.context_length == 10
assert not r.circular
assert r.start_index == 1
# Properties of circular region
r = Region(5, 9, context=Context(10, True, start_index=4))
assert r.start == 5
assert r.end == 9
assert r.context_length == 10
assert r.circular
assert r.start_index == 4
# Properties of circular region
r = Region(7,
5,
direction=Region.REVERSE,
context=Context(10, False, start_index=1))
assert r.start == 7
assert r.end == 5
assert r.context_length == 10
assert not r.circular
assert r.start_index == 1
def test_region_copy():
r = Region(50,
20,
context=Context(1000, False, 2),
name='name',
direction=Region.REVERSE)
r2 = r.copy()
assert r.same_context(r2)
def test_contig_constructor_with_context_error(query_subject_example):
"""This should raise a ContigError since the region lengths between
r1 and r2 are different"""
query, subject = query_subject_example
with pytest.raises(ContigError):
r1 = Region(1, 2, context=Context(100, True, start_index=1))
r2 = Region(1, 20, context=Context(100, True, start_index=1))
Contig(r1, r2, "Throws error")
def test_ends_overlap_with_raise_region_error():
"""This test should raise an error since the contexts are different"""
with pytest.raises(RegionError):
r = Region(10, 50, context=Context(100, False, start_index=0))
r2 = Region(20, 90, context=Context(100, True, start_index=0))
r.end_overlaps_with(r2)
with pytest.raises(RegionError):
r = Region(10, 50, context=Context(100, False, start_index=0))
r2 = Region(20, 90, context=Context(100, False, start_index=1))
r.end_overlaps_with(r2)
def test_self_circular_gap():
"""
context: |-------------------------|
r1: ----| |-----
r1.gap(r1) |>>>>>>>>>>>>|
"""
r1 = Region(80, 20, context=Context(100, True, start_index=0))
g = r1.get_gap(r1)
assert g.start == 21
assert g.end == 79
def test_overlap_circular():
"""
Tests overlap with circular regions
r1 ------| |-------
r2 ---------| |----
"""
r1 = Region(90, 10, context=Context(100, True, start_index=2))
r2 = Region(95, 20, context=Context(100, True, start_index=2))
overlap = r1.get_overlap(r2)
assert overlap.start == 95
assert overlap.end == 10
def test_str_and_repr():
linear_context = Context(100, False, 1)
r = Region.create_from_ends(5,
10,
linear_context,
direction=Region.FORWARD)
print(r)
print(str(r))
def test_lp_and_rp():
r = Region(1,
3,
direction=Region.FORWARD,
context=Context(9, True, start_index=1))
assert r.lp == 1
assert r.rp == 3
assert r.start == r.lp
assert r.end == r.rp
r = Region(3,
1,
direction=Region.REVERSE,
context=Context(9, False, start_index=1))
assert r.lp == 1
assert r.rp == 3
assert r.start == r.rp
assert r.end == r.lp
def test_region_schema():
c = Context(1000, True, start_index=2)
r = Region(5, 100, c, direction=Region.REVERSE, name="New region")
schema = schemas.RegionSchema()
data = schema.dump(r)
assert data['start'] == 5
assert data['end'] == 100
assert data['context']['length'] == 1000
assert data['direction'] == Region.REVERSE
assert data['length'] == len(r)
def test_region():
r = Region(2, 2, context=Context(3, True, start_index=1))
assert r.bounds_end == 3
s = 1
e = 2
l = 10
start_index = 1
r = Region(s, e, context=Context(l, True, start_index=start_index))
assert r.bounds_end == 10
assert r.bounds_start == start_index
indices = list(range(start_index - 3, start_index + l - 1 + 3))
values = list(range(start_index, l + start_index))
print(values)
assert len(values) == l
for x in range(start_index - 3, start_index + l - 1):
assert r.context.translate_pos(x) == values[x - start_index]
for x in range(start_index + l - 1, start_index + l - 1 + 3):
assert r.context.translate_pos(x) == values[x - start_index -
len(values)]
with pytest.raises(RegionError):
Region(500, 100, context=Context(1000, False))
start_index = 10
r = Region(100, 500, context=Context(1000, True, start_index=start_index))
assert r.bounds_start == start_index
assert r.bounds_end == start_index + r.context_length - 1
for x in range(-5, 300):
r = Region(100, x, context=Context(200, True, start_index=30))
assert r.end <= r.bounds_end
for x in range(-5, 300):
r = Region(x, 100, context=Context(200, True, start_index=30))
assert r.start >= r.bounds_start
def test_reverse_region():
s = 1
e = 5
l = 10
start_index = 0
r = Region(e,
s,
direction=Region.REVERSE,
context=Context(l, True, start_index=start_index))
print(r.start, r.end)
assert r.start == e
assert r.end == s
def test_end_setter():
r = Region(2, 5, context=Context(9, False, start_index=1))
r.left_end = 1
assert r.start == 1 == r.left_end == r.lp
r.right_end = 6
assert r.end == 6 == r.right_end == r.rp
r = Region(5,
2,
direction=Region.REVERSE,
context=Context(9, False, start_index=1))
r.left_end = 1
assert r.end == 1 == r.left_end == r.lp
r.right_end = 6
assert r.start == 6 == r.right_end == r.rp
def test_ends_overlap_with_reverse_regions():
"""This tests ends overlaps with reverse regions"""
r = Region(50,
10,
direction=Region.REVERSE,
context=Context(100, False, start_index=0))
r2 = Region(90,
20,
direction=Region.REVERSE,
context=Context(100, False, start_index=0))
assert r.end_overlaps_with(r2)
assert not r2.end_overlaps_with(r)
def test_overlap_linear_forward():
"""This tests that overlap region has basic attributes expected"""
r = Region(10, 50, context=Context(100, False, start_index=0))
r2 = Region(20, 90, context=Context(100, False, start_index=0))
overlap = r.get_overlap(r2)
print(overlap.start, overlap.end)
assert overlap.same_context(r)
assert overlap.same_context(r2)
assert overlap.start == 20
assert overlap.end == 50
assert overlap.direction == r.direction
assert r2.get_overlap(r) is None
def test_create_from_ends():
linear_context = Context(100, False, 1)
circular_context = Context(100, True, 1)
# Test forward, linear
r = Region.create_from_ends(5,
10,
linear_context,
direction=Region.FORWARD)
assert r.left_end == 5 == r.start
assert r.right_end == 10 == r.end
r = Region.create_from_ends(5,
10,
linear_context,
direction=Region.REVERSE)
assert r.left_end == 5 == r.end
assert r.right_end == 10 == r.start
# Test forward, linear with error
with pytest.raises(RegionError):
r = Region.create_from_ends(10,
5,
linear_context,
direction=Region.FORWARD)
with pytest.raises(RegionError):
r = Region.create_from_ends(10,
5,
linear_context,
direction=Region.REVERSE)
# when left end > right end is ALWAYS means its circular
r = Region.create_from_ends(10,
5,
circular_context,
direction=Region.FORWARD)
assert r.left_end == 10
assert r.right_end == 5
assert r.start == 10
assert r.end == 5
r = Region.create_from_ends(10,
5,
circular_context,
direction=Region.REVERSE)
assert r.left_end == 10
assert r.right_end == 5
assert r.start == 5
assert r.end == 10
def test_circular_gaps():
"""
context: |-------------------------|
r1: ----| |-----
r2: |----|
r1.get_gap(r2) |==|
r2.get_gap(r1) |==|
"""
r1 = Region(80, 20, context=Context(100, True, start_index=0))
r2 = Region(50, 60, context=Context(100, True, start_index=0))
g1 = r1.get_gap(r2)
assert g1.start == 21
assert g1.end == 49
g2 = r2.get_gap(r1)
assert g2.start == 61
assert g2.end == 79
def test_extend_end():
r = Region(40,
30,
direction=Region.REVERSE,
context=Context(100, True, start_index=1))
re = 15
le = 7
l = r.length
r.extend_right_end(re)
r.extend_left_end(le)
assert r.right_end == 40 + re
assert r.left_end == 30 - le
assert r.length == l + re + le
r = Region(40,
30,
direction=Region.REVERSE,
context=Context(100, True, start_index=1))
re = -3
le = -2
l = r.length
r.extend_right_end(re)
r.extend_left_end(le)
assert r.right_end == 40 + re
assert r.left_end == 30 - le
assert r.length == l + re + le
def test_extend_end():
# linear, forward
r = Region(10, 20, context=Context(100, False, start_index=1))
r.extend_end(5)
assert r.end == 25
# linear, reverse
r = Region(20,
10,
direction=Region.REVERSE,
context=Context(100, False, start_index=1))
r.extend_end(5)
assert r.end == 5
# linear, forward, negative
r = Region(10, 20, context=Context(100, False, start_index=1))
r.extend_end(-5)
assert r.end == 15
# linear, reverse, negative
r = Region(20,
10,
direction=Region.REVERSE,
context=Context(100, False, start_index=1))
r.extend_end(-5)
assert r.end == 15
# over origin, forward
r = Region(-5,
5,
direction=Region.FORWARD,
context=Context(100, True, start_index=1))
r.extend_end(-5)
assert r.end == 100
# Retract by length
r = Region(5,
10,
direction=Region.FORWARD,
context=Context(100, True, start_index=1))
r.extend_end(-r.length + 1)
assert r.start == r.end
# Raise error
r = Region(5,
10,
direction=Region.FORWARD,
context=Context(100, True, start_index=1))
with pytest.raises(RegionError):
r.extend_end(-r.length)
r = Region(2,
4,
direction=Region.FORWARD,
context=Context(12, True, start_index=1))
r.extend_end(9)
with pytest.raises(RegionError):
r.extend_end(10)
def test_region_gap_basic():
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(60, 70, context=Context(100, False, start_index=0))
g = r.get_gap(r2)
assert g.lp == 51
assert g.rp == 59
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(51, 70, context=Context(100, False, start_index=0))
assert r.get_gap(r2) is None
r = Region(90, 99, context=Context(100, False, start_index=1))
r2 = Region(2, 70, context=Context(100, False, start_index=1))
g = r.get_gap(r2)
assert g.start == 100
assert g.end == 1
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(48, 70, context=Context(100, False, start_index=0))
g = r.get_gap(r2)
assert g is None
def test_extend_start():
# linear, forward
r = Region(10, 20, context=Context(100, False, start_index=1))
r.extend_start(5)
assert r.start == 5
# linear, reverse
r = Region(20,
10,
direction=Region.REVERSE,
context=Context(100, False, start_index=1))
r.extend_start(5)
assert r.start == 25
# linear, forward, negative
r = Region(10, 20, context=Context(100, False, start_index=1))
r.extend_start(-5)
assert r.start == 15
# linear, reverse, negative
r = Region(20,
10,
direction=Region.REVERSE,
context=Context(100, False, start_index=1))
r.extend_start(-5)
assert r.start == 15
# over origin, forward
# 95 96 97 98 99 100 1 2 3 4
# -5 -4 -3 -2 -1 0
r = Region(-5,
5,
direction=Region.FORWARD,
context=Context(100, True, start_index=1))
r.extend_start(-6)
assert r.start == 1
# Retract by length
r = Region(5,
10,
direction=Region.FORWARD,
context=Context(100, True, start_index=1))
r.extend_start(-r.length + 1)
assert r.start == r.end
# Throw error
r = Region(5,
10,
direction=Region.FORWARD,
context=Context(100, True, start_index=1))
with pytest.raises(RegionError):
r.extend_start(-r.length)
r = Region(2,
4,
direction=Region.FORWARD,
context=Context(12, True, start_index=1))
r.extend_start(9)
with pytest.raises(RegionError):
r.extend_start(10)
def test_region_fuse():
# Fusing two linear regions
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(51, 70, context=Context(100, False, start_index=0))
assert r.consecutive_with(r2)
assert not r2.consecutive_with(r)
r.fuse(r2)
assert r2.fuse(r) is None
r = Region(95, 100, context=Context(100, True, start_index=1))
r2 = Region(1, 70, context=Context(100, True, start_index=1))
assert r.consecutive_with(r2)
assert not r2.consecutive_with(r)
r.fuse(r2)
assert r.start == 95
assert r.end == 70
assert r2.start == 1
assert r2.end == 70
r = Region(1, 100, context=Context(100, False, start_index=1))
r2 = Region(5, 99, context=Context(100, False, start_index=1))
assert not r.consecutive_with(r2)
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(51, 70, context=Context(100, False, start_index=0))
f = r.fuse(r2, inplace=False)
assert r is not f
def test_consecutive_with():
# is consecutive
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(51, 70, context=Context(100, False, start_index=0))
assert r.consecutive_with(r2)
assert not r2.consecutive_with(r)
# has gap
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(52, 70, context=Context(100, False, start_index=0))
assert not r.consecutive_with(r2)
assert not r2.consecutive_with(r)
# same indices
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(50, 70, context=Context(100, False, start_index=0))
assert not r.consecutive_with(r2)
assert not r2.consecutive_with(r)
# has overlap
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(49, 70, context=Context(100, False, start_index=0))
assert not r.consecutive_with(r2)
assert not r2.consecutive_with(r)
# linear regions over origin
r = Region(20, 100, context=Context(100, False, start_index=1))
r2 = Region(1, 10, context=Context(100, False, start_index=1))
assert not r.consecutive_with(r2)
assert not r2.consecutive_with(r)
# linear regions over origin
r = Region(1, 10, context=Context(100, False, start_index=1))
r2 = Region(11, 30, context=Context(100, False, start_index=1))
assert r.consecutive_with(r2)
assert not r2.consecutive_with(r)
# circular regions over origin
r = Region(20, 100, context=Context(100, True, start_index=1))
r2 = Region(1, 10, context=Context(100, True, start_index=1))
assert r.consecutive_with(r2)
assert not r2.consecutive_with(r)
# self consecutive with
r = Region(20, 19, context=Context(100, True))
assert r.consecutive_with(r)
with pytest.raises(RegionError):
r = Region(20, 50, context=Context(100, False, start_index=0))
r2 = Region(51, 70, context=Context(100, False, start_index=1))
r.consecutive_with(r2)
r = Region(90, 10, context=Context(100, True, start_index=1))
r2 = Region(11, 20, context=Context(100, True, start_index=1))
assert r.consecutive_with(r2)
assert not r2.consecutive_with(r)
r = Region(10,
90,
direction=Region.REVERSE,
context=Context(100, True, start_index=1))
r2 = Region(11,
20,
direction=Region.FORWARD,
context=Context(100, True, start_index=1))
assert r.consecutive_with(r2)
assert not r2.consecutive_with(r)
r = Region(10,
90,
direction=Region.REVERSE,
context=Context(100, True, start_index=1))
r2 = Region(89,
20,
direction=Region.REVERSE,
context=Context(100, True, start_index=1))
assert not r.consecutive_with(r2)
assert r2.consecutive_with(r)
def test_ends_overlaps_with():
r = Region(10, 50, context=Context(100, False, start_index=0))
r2 = Region(20, 90, context=Context(100, False, start_index=0))
assert r.end_overlaps_with(r2)
assert not r2.end_overlaps_with(r)
def test_raise_context_error():
with pytest.raises(RegionError):
r = Region(10, 50, context=Context(100, True, start_index=0))
r2 = Region(20, 90, context=Context(100, False, start_index=0))
r.consecutive_with(r2)
with pytest.raises(RegionError):
r = Region(10, 50, context=Context(100, False, start_index=0))
r2 = Region(20, 90, context=Context(101, False, start_index=0))
r.consecutive_with(r2)
with pytest.raises(RegionError):
r = Region(10, 50, context=Context(100, False, start_index=1))
r2 = Region(20, 90, context=Context(100, False, start_index=0))
r.consecutive_with(r2)
def test_gap_span():
r = Region(1, 100, context=Context(100, True, start_index=1))
r2 = Region(10, 90, context=Context(100, True, start_index=1))
assert r.get_gap_span(r2) is None
r = Region(1, 10, context=Context(100, True, start_index=1))
r2 = Region(10, 90, context=Context(100, True, start_index=1))
assert r.get_gap_span(r2) == -1
r = Region(1, 10, context=Context(100, True, start_index=1))
r2 = Region(11, 90, context=Context(100, True, start_index=1))
assert r.get_gap_span(r2) == 0
r = Region(1, 10, context=Context(100, True, start_index=1))
r2 = Region(8, 90, context=Context(100, True, start_index=1))
assert r.get_gap_span(r2) == -3
r = Region(1, 10, context=Context(100, True, start_index=1))
r2 = Region(15, 90, context=Context(100, True, start_index=1))
assert r.get_gap_span(r2) == 4
def test_ends_overlap_with_circular_context():
"""This tests handling of circular context with end overlaps"""
r = Region(90, 10, context=Context(100, True, start_index=2))
r2 = Region(5, 20, context=Context(100, True, start_index=2))
assert r.end_overlaps_with(r2)
assert not r2.end_overlaps_with(r)
def test_gap():
# Test when r2 is contained in r1
r = Region(1, 100, context=Context(100, True, start_index=1))
r2 = Region(10, 90, context=Context(100, True, start_index=1))
g = r.get_gap(r2)
assert g is None
# Test when r2 is contained in r1; test on end
r = Region(1, 100, context=Context(100, True, start_index=1))
r2 = Region(10, 100, context=Context(100, True, start_index=1))
g = r.get_gap(r2)
assert g is None
# Test when r2 is contained in r1; test on start
r = Region(1, 100, context=Context(100, True, start_index=1))
r2 = Region(1, 10, context=Context(100, True, start_index=1))
g = r.get_gap(r2)
assert g is None
r = Region(25, 90, context=Context(100, True, start_index=1))
r2 = Region(1, 10, context=Context(100, True, start_index=1))
# Test outer gap
g = r.get_gap(r2)
assert r.get_gap_span(r2) == g.length
assert r.get_gap_span(r2) == 10
# Test inner gap
g = r2.get_gap(r)
assert r2.get_gap_span(r) == g.length
assert g.length == 14
# Test overlap
r = Region(1, 10, context=Context(100, True, start_index=1))
r2 = Region(5, 15, context=Context(100, True, start_index=1))
g = r.get_gap(r2)
assert g is None
r = Region(1, 10, context=Context(100, True, start_index=1))
r2 = Region(10, 15, context=Context(100, True, start_index=1))
g = r.get_gap(r2)
assert g is None
def test_subregion():
r = Region(20, 50, context=Context(100, False, start_index=0))
r.sub_region(20, 30)
s = r.sub_region(30, 50)
assert s.start == 30
assert s.end == 50
with pytest.raises(RegionError):
r.sub_region(19, 30)
with pytest.raises(RegionError):
r.sub_region(30, 51)
r = Region(90, 10, context=Context(100, True, start_index=0))
s = r.sub_region(95, 5)
s_compare = Region(95, 5, context=Context(100, True, start_index=0))
assert s.start == 95
assert s.end == 5
assert s_compare.length == s.length
def test_eq_location():
r = Region(10, 20, context=Context(100, False, start_index=1))
r2 = Region(10, 20, context=Context(100, False, start_index=1))
r3 = Region(10, 20, context=Context(110, False, start_index=1))
assert r.equivalent_location(r2)
assert r2.equivalent_location(r)
with pytest.raises(RegionError):
r.equivalent_location(r3)
with pytest.raises(RegionError):
r3.equivalent_location(r)
def test_reverse_direction():
# is_forward and is_reverse
r = Region(10, 50, context=Context(100, False, start_index=0))
assert r.is_forward()
assert not r.is_reverse()
r = Region(50,
10,
direction=Region.REVERSE,
context=Context(100, False, start_index=0))
assert r.is_reverse()
assert not r.is_forward()
assert r.length == 41
# reverse_direction
r.reverse_direction()
assert r.is_forward()
assert not r.is_reverse()
assert r.length == 41
# reverse back
r.reverse_direction()
assert r.is_reverse()
assert not r.is_forward()
assert r.length == 41
r.set_forward()
assert r.is_forward()
assert r.length == 41
r.set_reverse()
assert r.is_reverse()
assert r.length == 41
r.set_reverse()
assert r.is_reverse()
assert r.length == 41