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KeyboardInterrupt Traceback (most recent call last)
<ipython-input-2-9b2386881473> in <module>()
----> 1 lo = LiftOver('hg19', 'mm10')
2 lo.convert_coordinate('chr1', 1000000)
~/anaconda3/lib/python3.6/site-packages/pyliftover/liftover.py in __init__(self, from_db, to_db, search_dir, cache_dir, use_web, write_cache, use_gzip)
60 # From- and To- db names were provided.
61 f = open_liftover_chain_file(from_db=from_db, to_db=to_db, search_dir=search_dir, cache_dir=cache_dir, use_web=use_web, write_cache=write_cache)
---> 62 self.chain_file = LiftOverChainFile(f)
63 f.close()
64
~/anaconda3/lib/python3.6/site-packages/pyliftover/chainfile.py in __init__(self, f)
101 '''
102 self.chains = self._load_chains(f)
--> 103 self.chain_index = self._index_chains(self.chains)
104
105 @staticmethod
~/anaconda3/lib/python3.6/site-packages/pyliftover/chainfile.py in _index_chains(chains)
146 tree = chain_index[c.source_name]
147 for (sfrom, sto, tfrom, tto) in c.blocks:
--> 148 tree.add_interval(sfrom, sto, (tfrom, tto, c))
149
150 # Sort all interval trees
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
83 if self.right_subtree is None:
84 self.right_subtree = IntervalTree(self.center, self.max)
---> 85 self.right_subtree.add_interval(start, end, data)
86 else:
87 self.mid_sorted_by_start.append((start, end, data))
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
83 if self.right_subtree is None:
84 self.right_subtree = IntervalTree(self.center, self.max)
---> 85 self.right_subtree.add_interval(start, end, data)
86 else:
87 self.mid_sorted_by_start.append((start, end, data))
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
83 if self.right_subtree is None:
84 self.right_subtree = IntervalTree(self.center, self.max)
---> 85 self.right_subtree.add_interval(start, end, data)
86 else:
87 self.mid_sorted_by_start.append((start, end, data))
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
83 if self.right_subtree is None:
84 self.right_subtree = IntervalTree(self.center, self.max)
---> 85 self.right_subtree.add_interval(start, end, data)
86 else:
87 self.mid_sorted_by_start.append((start, end, data))
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
83 if self.right_subtree is None:
84 self.right_subtree = IntervalTree(self.center, self.max)
---> 85 self.right_subtree.add_interval(start, end, data)
86 else:
87 self.mid_sorted_by_start.append((start, end, data))
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
83 if self.right_subtree is None:
84 self.right_subtree = IntervalTree(self.center, self.max)
---> 85 self.right_subtree.add_interval(start, end, data)
86 else:
87 self.mid_sorted_by_start.append((start, end, data))
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
83 if self.right_subtree is None:
84 self.right_subtree = IntervalTree(self.center, self.max)
---> 85 self.right_subtree.add_interval(start, end, data)
86 else:
87 self.mid_sorted_by_start.append((start, end, data))
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
83 if self.right_subtree is None:
84 self.right_subtree = IntervalTree(self.center, self.max)
---> 85 self.right_subtree.add_interval(start, end, data)
86 else:
87 self.mid_sorted_by_start.append((start, end, data))
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
67 elif self.single_interval == 0:
68 # This is a usual tree, use standard addition method
---> 69 self._add_interval(start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
83 if self.right_subtree is None:
84 self.right_subtree = IntervalTree(self.center, self.max)
---> 85 self.right_subtree.add_interval(start, end, data)
86 else:
87 self.mid_sorted_by_start.append((start, end, data))
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
72 self._add_interval(*self.single_interval)
73 self.single_interval = 0
---> 74 self._add_interval(start, end, data)
75
76 def _add_interval(self, start, end, data=None):
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
79 if self.left_subtree is None:
80 self.left_subtree = IntervalTree(self.min, self.center)
---> 81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
83 if self.right_subtree is None:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in add_interval(self, start, end, data)
70 else:
71 # This is a tree with a single interval. Convert to a usual tree.
---> 72 self._add_interval(*self.single_interval)
73 self.single_interval = 0
74 self._add_interval(start, end, data)
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in _add_interval(self, start, end, data)
78 # Insert into left subtree
79 if self.left_subtree is None:
---> 80 self.left_subtree = IntervalTree(self.min, self.center)
81 self.left_subtree.add_interval(start, end, data)
82 elif start > self.center:
~/anaconda3/lib/python3.6/site-packages/pyliftover/intervaltree.py in __init__(self, min, max)
39 '''
40
---> 41 def __init__(self, min, max):
42 '''
43 Creates a tree node for keeping intervals somewhere in the range [min...max).
KeyboardInterrupt: