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import os
import sys
import unittest
try:
sys.path.insert(0, os.path.dirname(os.path.dirname(__file__)))
except Exception:
sys.path.insert(0, os.path.dirname(os.path.abspath(".")))
from bx.intervals.intersection import (
Interval,
IntervalNode,
IntervalTree,
)
class NeighborTestCase(unittest.TestCase):
def setUp(self):
iv = IntervalNode(50, 59, Interval(50, 59))
for i in range(0, 110, 10):
if i == 50:
continue
f = Interval(i, i + 9)
iv = iv.insert(f.start, f.end, f)
self.intervals = iv
def test_left(self):
iv = self.intervals
self.assertEqual(str(iv.left(60, n=2)), str([Interval(50, 59), Interval(40, 49)]))
for i in range(10, 100, 10):
r = iv.left(i, max_dist=10, n=1)
self.assertEqual(r[0].end, i - 1)
def test_toomany(self):
iv = self.intervals
self.assertEqual(len(iv.left(60, n=200)), 6)
def test_right(self):
iv = self.intervals
self.assertEqual(str(iv.left(60, n=2)), str([Interval(50, 59), Interval(40, 49)]))
def get_right_start(b10):
r = iv.right(b10 + 1, n=1)
assert len(r) == 1
return r[0].start
for i in range(10, 100, 10):
self.assertEqual(get_right_start(i), i + 10)
for i in range(0, 100, 10):
r = iv.right(i - 1, max_dist=10, n=1)
print(r)
self.assertEqual(r[0].start, i)
class UpDownStreamTestCase(unittest.TestCase):
def setUp(self):
iv = IntervalTree()
iv.add_interval(Interval(50, 59))
for i in range(0, 110, 10):
if i == 50:
continue
f = Interval(i, i + 9)
iv.add_interval(f)
self.intervals = iv
def test_upstream(self):
iv = self.intervals
upstreams = iv.upstream_of_interval(Interval(59, 60), num_intervals=200)
for u in upstreams:
self.assertTrue(u.end < 59)
upstreams = iv.upstream_of_interval(Interval(60, 70, strand=-1), num_intervals=200)
for u in upstreams:
self.assertTrue(u.start > 70)
upstreams = iv.upstream_of_interval(Interval(58, 58, strand=-1), num_intervals=200)
for u in upstreams:
self.assertTrue(u.start > 59)
def test_downstream(self):
iv = self.intervals
downstreams = iv.downstream_of_interval(Interval(59, 60), num_intervals=200)
for d in downstreams:
self.assertTrue(d.start > 60)
downstreams = iv.downstream_of_interval(Interval(59, 60, strand=-1), num_intervals=200)
for d in downstreams:
self.assertTrue(d.start < 59)
def test_n(self):
iv = self.intervals
for i in range(0, 90, 10):
r = iv.after(i, max_dist=20, num_intervals=2)
self.assertEqual(r[0].start, i + 10)
self.assertEqual(r[1].start, i + 20)
r = iv.after_interval(Interval(i, i), max_dist=20, num_intervals=2)
self.assertEqual(r[0].start, i + 10)
self.assertEqual(r[1].start, i + 20)
class LotsaTestCase(unittest.TestCase):
"""put lotsa data in the tree and make sure it works"""
def setUp(self):
iv = IntervalNode(1, 2, Interval(1, 2))
self.max = 1000000
for i in range(0, self.max, 10):
f = Interval(i, i)
iv = iv.insert(f.start, f.end, f)
for i in range(600):
iv = iv.insert(0, 1, Interval(0, 1))
self.intervals = iv
def test_count(self):
iv = self.intervals
r = iv.right(1, n=33)
self.assertEqual(len(r), 33)
l = iv.left(1, n=33)
self.assertEqual(len(l), 1)
u = iv.right(1, n=9999)
self.assertEqual(len(u), 250)
# now increase max_dist
u = iv.right(1, n=9999, max_dist=99999)
self.assertEqual(len(u), 9999)
def test_max_dist(self):
iv = self.intervals
r = iv.right(1, max_dist=0, n=10)
self.assertEqual(len(r), 0)
for n, d in enumerate(range(10, 1000, 10)):
r = iv.right(1, max_dist=d, n=10000)
self.assertEqual(len(r), n + 1)
def test_find(self):
iv = self.intervals
path = sys.path[:]
sys.path = sys.path[2:]
random = __import__("random")
sys.path = path
for t in range(25):
start = random.randint(0, self.max - 10000)
end = start + random.randint(100, 10000)
results = iv.find(start, end)
for feat in results:
self.assertTrue((feat.end >= start and feat.end <= end) or (feat.start <= end and feat.start >= start))
class IntervalTreeTest(unittest.TestCase):
def setUp(self):
iv = IntervalTree()
n = 0
for i in range(1, 1000, 80):
iv.insert(i, i + 10, {"value": i * i})
# add is synonym for insert.
iv.add(i + 20, i + 30, {"astr": str(i * i)})
# or insert/add an interval object with start, end attrs.
iv.insert_interval(Interval(i + 40, i + 50, value={"astr": str(i * i)}))
iv.add_interval(Interval(i + 60, i + 70, value={"astr": str(i * i)}))
n += 4
self.intervals = self.iv = iv
self.nintervals = n
def test_find(self):
r = self.iv.find(100, 200)
self.assertEqual(len(r), 5)
def test_traverse(self):
a = []
fn = a.append
self.iv.traverse(fn)
self.assertEqual(len(a), self.nintervals)
def test_empty(self):
iv = IntervalTree()
self.assertEqual([], iv.find(100, 300))
self.assertEqual([], iv.after(100))
self.assertEqual([], iv.before(100))
self.assertEqual([], iv.after_interval(100))
self.assertEqual([], iv.before_interval(100))
self.assertEqual([], iv.upstream_of_interval(100))
self.assertEqual([], iv.downstream_of_interval(100))
self.assertEqual(None, iv.traverse(lambda x: x.append(1)))
def test_public_interval(self):
def fn(ival):
return self.assertTrue(ival.interval)
self.iv.traverse(fn)
if __name__ == "__main__":
unittest.main()
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