https://github.com/brentp/quicksect

a cythonized, extended version of the interval search tree in bx
https://github.com/brentp/quicksect

Last synced: 3 months ago
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a cythonized, extended version of the interval search tree in bx

• Host: GitHub
• URL: https://github.com/brentp/quicksect
• Owner: brentp
• License: mit
• Created: 2008-10-29T18:34:20.000Z (over 16 years ago)
• Default Branch: master
• Last Pushed: 2019-06-04T16:42:09.000Z (about 6 years ago)
• Last Synced: 2025-03-18T02:12:19.730Z (3 months ago)
• Language: Python
• Homepage:
• Size: 18.6 KB
• Stars: 30
• Watchers: 4
• Forks: 7
• Open Issues: 4
• Metadata Files:
  • Readme: README.rst
  • License: LICENSE

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README

        
Quicksect

=========

.. image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.png

    :target: http://bioconda.github.io/recipes/quicksect/README.html

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.

License is MIT.

Installation

------------

    pip install quicksect

or

    conda install -c bioconda quicksect

Use

---

    >>> 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)]