Metadata-Version: 1.1
Name: intervaltree-bio
Version: 0.6
Summary: Interval tree convenience classes for genomic data
Home-page: https://github.com/konstantint/intervaltree-bio
Author: Konstantin Tretyakov
Author-email: kt@ut.ee
License: MIT
Description: ================
        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>`__.
        
Keywords: interval-tree data-structure intervals tree genomics bioinformatics ucsc
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development :: Libraries
