Skip to main content

fast, simple interval intersection

Project description

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

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)]

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
quicksect-0.2.0.tar.gz (65.7 kB) Copy SHA256 hash SHA256 Source None Jul 19, 2018

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page