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Intervaltree-Bio
================
Convenience classes for loading UCSC genomic annotation records into a set of `interval tree <https://pypi.python.org/pypi/intervaltree>`__ 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 <http://genome.ucsc.edu/>`__.
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 <https://github.com/konstantint/intervaltree-bio>`__.
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