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"""
Intersects ... faster. Suports GenomicInterval datatype and multiple
chromosomes.
"""
import math
import random
try:
from time import process_time
except ImportError:
# For compatibility with Python < 3.3
from time import clock as process_time
class IntervalTree:
def __init__(self):
self.chroms = {}
def insert(self, interval, linenum=0, other=None):
chrom = interval.chrom
start = interval.start
end = interval.end
if interval.chrom in self.chroms:
self.chroms[chrom] = self.chroms[chrom].insert(start, end, linenum, other)
else:
self.chroms[chrom] = IntervalNode(start, end, linenum, other)
def intersect(self, interval, report_func):
chrom = interval.chrom
start = interval.start
end = interval.end
if chrom in self.chroms:
self.chroms[chrom].intersect(start, end, report_func)
def traverse(self, func):
for item in self.chroms.values():
item.traverse(func)
class IntervalNode:
def __init__(self, start, end, linenum=0, other=None):
# Python lacks the binomial distribution, so we convert a
# uniform into a binomial because it naturally scales with
# tree size. Also, python's uniform is perfect since the
# upper limit is not inclusive, which gives us undefined here.
self.priority = math.ceil((-1.0 / math.log(0.5)) * math.log(-1.0 / (random.uniform(0, 1) - 1)))
self.start = start
self.end = end
self.maxend = self.end
self.minend = self.end
self.left = None
self.right = None
self.linenum = linenum
self.other = other
def insert(self, start, end, linenum=0, other=None):
root = self
if start > self.start:
# insert to right tree
if self.right:
self.right = self.right.insert(start, end, linenum, other)
else:
self.right = IntervalNode(start, end, linenum, other)
# rebalance tree
if self.priority < self.right.priority:
root = self.rotateleft()
else:
# insert to left tree
if self.left:
self.left = self.left.insert(start, end, linenum, other)
else:
self.left = IntervalNode(start, end, linenum, other)
# rebalance tree
if self.priority < self.left.priority:
root = self.rotateright()
if root.right and root.left:
root.maxend = max(root.end, root.right.maxend, root.left.maxend)
root.minend = min(root.end, root.right.minend, root.left.minend)
elif root.right:
root.maxend = max(root.end, root.right.maxend)
root.minend = min(root.end, root.right.minend)
elif root.left:
root.maxend = max(root.end, root.left.maxend)
root.minend = min(root.end, root.left.minend)
return root
def rotateright(self):
root = self.left
self.left = self.left.right
root.right = self
if self.right and self.left:
self.maxend = max(self.end, self.right.maxend, self.left.maxend)
self.minend = min(self.end, self.right.minend, self.left.minend)
elif self.right:
self.maxend = max(self.end, self.right.maxend)
self.minend = min(self.end, self.right.minend)
elif self.left:
self.maxend = max(self.end, self.left.maxend)
self.minend = min(self.end, self.left.minend)
return root
def rotateleft(self):
root = self.right
self.right = self.right.left
root.left = self
if self.right and self.left:
self.maxend = max(self.end, self.right.maxend, self.left.maxend)
self.minend = min(self.end, self.right.minend, self.left.minend)
elif self.right:
self.maxend = max(self.end, self.right.maxend)
self.minend = min(self.end, self.right.minend)
elif self.left:
self.maxend = max(self.end, self.left.maxend)
self.minend = min(self.end, self.left.minend)
return root
def intersect(self, start, end, report_func):
if start < self.end and end > self.start:
report_func(self)
if self.left and start < self.left.maxend:
self.left.intersect(start, end, report_func)
if self.right and end > self.start:
self.right.intersect(start, end, report_func)
def traverse(self, func):
if self.left:
self.left.traverse(func)
func(self)
if self.right:
self.right.traverse(func)
def main():
test = None
intlist = []
for _ in range(20000):
start = random.randint(0, 1000000)
end = start + random.randint(1, 1000)
if test:
test = test.insert(start, end)
else:
test = IntervalNode(start, end)
intlist.append((start, end))
starttime = process_time()
for x in range(5000):
start = random.randint(0, 10000000)
end = start + random.randint(1, 1000)
result = []
test.intersect(start, end, lambda x: result.append(x.linenum))
print("%f for tree method" % (process_time() - starttime))
starttime = process_time()
for _ in range(5000):
start = random.randint(0, 10000000)
end = start + random.randint(1, 1000)
bad_sect(intlist, start, end)
print("%f for linear (bad) method" % (process_time() - starttime))
def test_func(node):
print("[%d, %d), %d" % (node.start, node.end, node.maxend))
def bad_sect(lst, int_start, int_end):
intersection = []
for start, end in lst:
if int_start < end and int_end > start:
intersection.append((start, end))
return intersection
if __name__ == "__main__":
main()
|
