Quicksect
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)]
1 maintainer
Metadata
1 maintainer
Release files for quicksect 0.2.2
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