class EmptyTreeTestCase(unittest.TestCase): """ test search on an empty tree.""" def setUp(self): self.tree = IntervalTree() def test_search(self): self.tree.search(46, 47) def test_find(self): self.tree.find(Interval(46, 47)) def test_left(self): self.tree.left(Interval(46, 47)) def test_right(self): self.tree.right(Interval(46, 47))
background = pd.read_table(b, sep="\t", usecols=[1, 2], header=None, names="Start End".split(), engine="c", dtype={ "Start": np.int32, "End": np.int32 }) tree = IntervalTree() for start_, end_ in zip(background.Start, background.End): tree.add(start_, end_) start = time() results = [] for start_, end_ in zip(chip.Start, chip.End): results.append(tree.search(start_, end_)) end = time() # print(result) total = end - start total_dt = datetime.datetime.fromtimestamp(total) minutes_seconds = total_dt.strftime('%-M.%-S.%f') open(snakemake.output[0], "w+").write(minutes_seconds)