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fast, simple interval intersection

Project description

Description

Quicksect is a fast python / cython implementation of interval search based on the pure python version in bx-python I pulled it out, optimized and converted to cython and James Taylor has incoporated it back into bx-python with his improvements.

I have brought this project back from the dead because I want a fast, simple, no-dependencies Interval tree.

Extended with removal operations and allows pretty print to display tree structure (By Jianlin)

License is MIT.

Installation

pip install quicksect

or

conda install -c bioconda quicksect

Use

To use extended quicksect(quicksectx):

>>> from quicksectx import IntervalNode, IntervalTree, Interval
>>> tree = IntervalTree()
>>> tree.add(1, 3, 100)
>>> tree.add(3, 7, 110)
>>> tree.add(2, 5, 120)
>>> tree.add(4, 6, 130)
>>> print(tree.pretty_print())
Inv(1, 3, d=100)
r:  Inv(3, 7, d=110)
l:    Inv(2, 5, d=120)
r:    Inv(4, 6, d=130)
>>> print(tree.find(Interval(2, 5)))
[Inv(1, 3, d=100), Inv(3, 7, d=110), Inv(2, 5, d=120), Inv(4, 6, d=130)]
>>> tree.remove(Interval(2, 5))
>>> print(tree.find(Interval(2, 5)))
[Inv(1, 3, d=100), Inv(3, 7, d=110), Inv(4, 6, d=130)]

To use traditional quicksect, you can still using the same syntax:

>>> from quicksect import IntervalNode, Interval, IntervalTree

Most common use will be via IntervalTree:

>>> tree = IntervalTree()
>>> tree.add(23, 45)
>>> tree.add(55, 66)
>>> tree.search(46, 47)
[]
>>> tree.search(44, 56)
[Interval(55, 66), Interval(23, 45)]
>>> tree.insert(Interval(88, 444))
>>> res = tree.find(Interval(99, 100))
>>> res
[Interval(88, 444)]
>>> res[0].start, res[0].end
(88, 444)

Thats pretty much everything you need to know about the tree.

Test

$ python setup.py test

Low-Level

In some cases, users may want to utilize the lower-level interface that accesses the nodes of the tree:

>>> inter = IntervalNode(Interval(22, 33))
>>> inter = inter.insert(Interval(44, 55))
>>> inter.intersect(24, 26)
[Interval(22, 33)]
>>> inter.left(Interval(34, 35), n=1)
[Interval(22, 33)]
>>> inter.right(Interval(34, 35), n=1)
[Interval(44, 55)]

Project details


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