# 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()