def test_lp_and_rp_setter():
r = Region(1,
3,
direction=Region.FORWARD,
context=Context(9, False, start_index=1))
r.lp = 2
assert r.lp == 2
r.rp = 5
assert r.rp == 5
r.rp = 4
r = Region(3,
1,
direction=Region.REVERSE,
context=Context(9, False, start_index=1))
r.lp = 2
assert r.lp == 2
r.rp = 5
assert r.rp == 5
r.rp = 4
r = Region(2, 2, context=Context(9, False, start_index=1))
r.rp = 3
assert r.rp == 3 == r.lp
r.lp = 4
assert r.rp == 4 == r.lp
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_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 query_subject_example(scope="module"):
"""This fixture returns an example of a subject and query"""
subject = ContigRegion(911, 757, Context(9795, True), name="subjectexample", forward=False,
filename="templates/pRIAS (CC15).gb")
query = ContigRegion(1, 155, Context(22240, True), name="queryexample", forward=True,
filename="templates/pRasdfasdfaIAS (CC15).gb")
return [query, subject]
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_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_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_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_subquery():
c1 = Context(10000, True)
c2 = Context(5000, True)
q1 = ContigRegion(100, 300, context=c1, forward=True)
s1 = ContigRegion(500, 700, context=c2, forward=True)
contig = Contig(q1, s1, "BLAST")
sub_query1 = contig.sub_query(200, 250)
sub_query2 = contig.sub_query(220, 300)
assert len(sub_query1) == 51
assert len(sub_query2) == 81
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_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_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_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_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_context_schema():
c = Context(1000, True, start_index=2)
schema = schemas.ContextSchema()
data = schema.dump(c)
assert data['circular']
assert data['size'] == 1000
assert data['start'] == 2
def test_fuse():
# Test fuse
c1 = Context(10000, True)
c2 = Context(5100, True)
q1 = ContigRegion(100, 300, context=c1, forward=True)
q2 = ContigRegion(301, 600, context=c1, forward=True)
q3 = ContigRegion(301, 600, context=c2, forward=True)
s1 = ContigRegion(500, 700, context=c2, forward=True)
s2 = ContigRegion(701, 1000, context=c2, forward=True)
s3 = ContigRegion(701, 1000, context=c2, forward=True)
contig1 = Contig(q1, s1, "BLAST")
contig2 = Contig(q2, s2, "BLAST")
contig1.fuse(contig2)
assert contig1.query.end == 600
# Raises error if one has sequence and other does not
contig1 = Contig(q1, s1, "BLAST")
contig2 = Contig(q2, s2, "BLAST")
a = "A"*contig1.query.length
b = "B"*contig1.subject.length
c = "C"*contig2.query.length
d = "D"*contig2.subject.length
contig1.query.sequence = a
contig1.subject.sequence = b
contig2.query.sequence = c
contig2.subject.sequence = d
contig1.fuse(contig2)
assert contig1.query.sequence == a + c
assert contig1.subject.sequence == b + d
# Raises error if one has sequence and other does not
contig1 = Contig(q1, s1, "BLAST")
contig2 = Contig(q2, s2, "BLAST")
contig1.query.sequence = "AGTCTGAGCTGTCGTGATAGTGCTGA"
contig1.subject.sequence = "AGTYAGYCHYAYHCYHYSCHYHAYCY"
with pytest.raises(ContigError):
contig1.fuse(contig2)
# Raise error if different contexts
contig1 = Contig(q1, s1, "BLAST")
contig2 = Contig(q2, s2, "BLAST")
contig3 = Contig(q3, s3, "BLAST")
with pytest.raises(ContigError):
contig3.fuse(contig2)
def test_gap_cost_both_extendable():
subject = ContigRegion(1, 100, Context(9795, True))
query_context = Context(20000, True)
query = ContigRegion(1, 100, query_context)
left = BlastContig(query, subject, "test")
from matplotlib import pyplot as plt
for left_extendable, right_extendable, color in [(True, True, "blue"),
(False, True, "green"),
(False, False, "red")]:
X = []
Y = []
left.lp_extendable = left_extendable
left.rp_extendable = left_extendable
for right_start in range(1, 1000):
right = BlastContig(
ContigRegion(right_start, right_start + 99, query_context),
subject, "test")
right.lp_extendable = right_extendable
right.rp_extendable = right_extendable
gap_cost = Assembly._gap_cost(left, right)
left_end = left.query.end
right_start = right.query.start
distance = right_start - left_end
print(
f"{left_end} {right_start} Distance: {distance}, Gap_cost: {gap_cost}"
)
X.append(distance)
Y.append(gap_cost)
plt.scatter(X,
Y,
s=1.0,
c=[color] * len(Y),
label=f"{left_extendable + right_extendable}")
if False:
plt.ylim(0, 500)
plt.xlabel("Distance (bp)")
plt.ylabel("Gap Cost ($)")
plt.legend(loc=2)
plt.show()
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_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_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_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_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_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_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_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_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_contig_schema():
c1 = Context(10000, True)
c2 = Context(5100, True)
q1 = ContigRegion(100, 300, context=c1, forward=True)
s1 = ContigRegion(500, 700, context=c2, forward=True)
contig1 = Contig(q1, s1, "BLAST", data1=5)
schema = schemas.ContigSchema()
data = schema.dump(contig1)
assert data['query']['start'] == 100
assert data['query']['end'] == 300
assert data['query']['context']['length'] == 10000
assert data['subject']['start'] == 500
assert data['subject']['end'] == 700
assert data['subject']['context']['length'] == 5100
assert data['quality']
assert data['metadata'] == {'data1': 5}
assert data['alignment_length'] == 201
def test_divide_contigs():
c1 = Context(10000, True)
c2 = Context(8000, True)
q1 = ContigRegion(1000, 3000, context=c1, forward=True)
s1 = ContigRegion(5000, 7000, context=c2, forward=True)
contig = Contig(q1, s1, "BLAST")
# not including self
divided_contigs = contig.divide_contig(
[1100, 1200],
[2000, 2200, 2300],
include_self=False)
assert len(divided_contigs) == 12
# including self
divided_contigs = contig.divide_contig(
[1100, 1200],
[2000, 2200, 2300],
include_self=True)
assert len(divided_contigs) == 13
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