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# checklist.py:CopyrightHeadersValidator IGNORE
# ----------------------------------------------------------------------------
# This code is taken from bx-python project and added with a test for a new
# function `update` from line 195 to 211. The license for this code is
# included in licenses/bx_python.txt.
# ----------------------------------------------------------------------------
import sys
import unittest
import random
from skbio.metadata._intersection import IntervalObj
from skbio.metadata._intersection import IntervalNode
from skbio.metadata._intersection import IntervalTree
# Note: More bounds checking on input parameters are performed
# within test_interval.py
class NeighborTestCase(unittest.TestCase):
def setUp(self):
iv = IntervalNode(50, 59, IntervalObj(50, 59))
for i in range(0, 110, 10):
if i == 50:
continue
f = IntervalObj(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([IntervalObj(50, 59), IntervalObj(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([IntervalObj(50, 59), IntervalObj(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)
self.assertEqual(r[0].start, i)
class UpDownStreamTestCase(unittest.TestCase):
def setUp(self):
iv = IntervalTree()
iv.add_interval(IntervalObj(50, 59))
for i in range(0, 110, 10):
if i == 50:
continue
f = IntervalObj(i, i + 9)
iv.add_interval(f)
self.intervals = iv
def test_upstream(self):
iv = self.intervals
upstreams = iv.upstream_of_interval(IntervalObj(59, 60),
num_intervals=200)
for u in upstreams:
self.assertTrue(u.end < 59)
upstreams = iv.upstream_of_interval(IntervalObj(60, 70, strand=-1),
num_intervals=200)
for u in upstreams:
self.assertTrue(u.start > 70)
upstreams = iv.upstream_of_interval(IntervalObj(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(IntervalObj(59, 60),
num_intervals=200)
for d in downstreams:
self.assertTrue(d.start > 60)
downstreams = iv.downstream_of_interval(IntervalObj(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(IntervalObj(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, IntervalObj(1, 2))
self.max = 1000000
for i in range(0, self.max, 10):
f = IntervalObj(i, i)
iv = iv.insert(f.start, f.end, f)
for i in range(600):
iv = iv.insert(0, 1, IntervalObj(0, 1))
self.intervals = iv
def test_count(self):
iv = self.intervals
r = iv.right(1, n=33)
self.assertEqual(len(r), 33)
left = iv.left(1, n=33)
self.assertEqual(len(left), 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:]
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, dict(value=i*i))
# add is synonym for insert.
iv.add(i + 20, i + 30, dict(astr=str(i*i)))
# or insert/add an interval object with start, end attrs.
iv.insert_interval(IntervalObj(i + 40, i + 50,
value=dict(astr=str(i*i))))
iv.add_interval(IntervalObj(i + 60, i + 70,
value=dict(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_edge_cases(self):
iv = IntervalTree()
iv.insert(1, 1, 'foo')
iv.insert(3, 7, 'spam')
iv.insert(8, 8, 'abc')
self.assertEqual(iv.find(0, 1), [])
self.assertEqual(iv.find(1, 1), ['foo'])
self.assertEqual(iv.find(1, 2), ['foo'])
self.assertEqual(iv.find(2, 3), [])
self.assertEqual(iv.find(3, 3), ['spam'])
self.assertEqual(iv.find(3, 4), ['spam'])
self.assertEqual(iv.find(6, 7), ['spam'])
self.assertEqual(iv.find(7, 7), [])
self.assertEqual(iv.find(0, 8), ['foo', 'spam'])
self.assertEqual(iv.find(8, 8), ['abc'])
self.assertEqual(iv.find(8, 9), ['abc'])
self.assertEqual(iv.find(9, 9), [])
self.assertEqual(iv.find(0, 10), ['foo', 'spam', 'abc'])
self.assertEqual(iv.find(6, 10), ['spam', 'abc'])
self.assertEqual(iv.find(7, 9), ['abc'])
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):
self.iv.traverse(lambda ival: self.assertTrue(ival.interval))
def test_update(self):
i = 1
self.iv.update(i, i + 10, dict(value=i*i), dict(value=-1))
self.assertEqual([dict(value=-1)], self.iv.find(i, i+10))
if __name__ == "__main__":
unittest.main()
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