brentp / Quicksect
Programming Languages
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 <http://bx-python.trac.bx.psu.edu/>
__
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)]