Description:
intervaltree bio 1.0.1
Convenience classes for loading UCSC genomic annotation records into a set of interval tree data structures.
Installation
The easiest way to install most Python packages is via easy_install or pip:
$ pip install intervaltree-bio
The package requires the intervaltree package (which is normally installed automatically when using pip or easy_install).
Usage
One of the major uses for Interval tree data structures is in bioinformatics, where the
intervals correspond to genes or other features of the genome.
As genomes typically consist of a set of chromosomes, a separate interval tree for each
chromosome has to be maintained. Thus, rather than using an single interval tree, you would typically use
something like defaultdict(IntervalTree) to index data of genomic features.
The module intervaltree_bio offers a GenomeIntervalTree data structure, which is a similar convenience
data structure. In addition to specific methods for working with genomic intervals it also
provides facilities for reading BED files and the refGene table from UCSC.
The core example is loading the transcription regions of the knownGene table from the UCSC website:
>> from intervaltree_bio import GenomeIntervalTree
>> knownGene = GenomeIntervalTree.from_table()
>> len(knownGene)
It is then possible to use the data structure to search known genes within given intervals:
>> result = knownGene[b'chr1'].search(100000, 138529)
It is possible to load other UCSC tables besides knownGene or specify custom URL or file to read the table from.
Consult the docstring of the GenomeIntervalTree.from_table method for more details.
Copyright
Copyright (c) Konstantin Tretyakov
MIT license.
Report issues via Github.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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