{
    "info": {
        "author": "Konstantin Tretyakov",
        "author_email": "kt@ut.ee",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries"
        ],
        "description": "================\nIntervaltree-Bio\n================\n\nConvenience classes for loading UCSC genomic annotation records into a set of `interval tree <https://pypi.python.org/pypi/intervaltree>`__ data structures.\n\nInstallation\n------------\n\nThe easiest way to install most Python packages is via ``easy_install`` or ``pip``::\n\n    $ pip install intervaltree-bio\n\nThe package requires the ``intervaltree`` package (which is normally installed automatically when using ``pip`` or ``easy_install``).\n\nUsage\n--------\n\nOne of the major uses for Interval tree data structures is in bioinformatics, where the\nintervals correspond to genes or other features of the genome.\n\nAs genomes typically consist of a set of *chromosomes*, a separate interval tree for each\nchromosome has to be maintained. Thus, rather than using an single interval tree, you would typically use\nsomething like ``defaultdict(IntervalTree)`` to index data of genomic features.\nThe module ``intervaltree_bio`` offers a ``GenomeIntervalTree`` data structure, which is a similar convenience\ndata structure. In addition to specific methods for working with genomic intervals it also\nprovides facilities for reading BED files and the refGene table from `UCSC <http://genome.ucsc.edu/>`__.\n\nThe core example is loading the transcription regions of the ``knownGene`` table from the UCSC website::\n\n    >> from intervaltree_bio import GenomeIntervalTree\n    >> knownGene = GenomeIntervalTree.from_table()\n    >> len(knownGene)\n\nIt is then possible to use the data structure to search known genes within given intervals::\n\n    >> result = knownGene[b'chr1'].search(100000, 138529)\n    \nIt is possible to load other UCSC tables besides ``knownGene`` or specify custom URL or file to read the table from.\nConsult the docstring of the ``GenomeIntervalTree.from_table`` method for more details.\n\nCopyright\n----------\n\n  * Copyright (c) Konstantin Tretyakov\n  * MIT license.\n  * Report issues via `Github <https://github.com/konstantint/intervaltree-bio>`__.",
        "description_content_type": null,
        "docs_url": null,
        "download_url": "UNKNOWN",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://github.com/konstantint/intervaltree-bio",
        "keywords": "interval-tree data-structure intervals tree genomics bioinformatics ucsc",
        "license": "MIT",
        "maintainer": null,
        "maintainer_email": null,
        "name": "intervaltree_bio",
        "package_url": "https://pypi.org/project/intervaltree_bio/",
        "platform": "UNKNOWN",
        "project_url": "https://pypi.org/project/intervaltree_bio/",
        "project_urls": {
            "Download": "UNKNOWN",
            "Homepage": "https://github.com/konstantint/intervaltree-bio"
        },
        "release_url": "https://pypi.org/project/intervaltree_bio/1.0.1/",
        "requires_dist": null,
        "requires_python": null,
        "summary": "Interval tree convenience classes for genomic data",
        "version": "1.0.1"
    },
    "last_serial": 1400542,
    "releases": {
        "1.0.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "a794df30f4ea784ee39baaf24c14a506",
                    "sha256": "e3458163528224c5680807e38388fff84656a4a1aa9e5d406d2ed0c59f1d329e"
                },
                "downloads": -1,
                "filename": "intervaltree_bio-1.0.0.zip",
                "has_sig": false,
                "md5_digest": "a794df30f4ea784ee39baaf24c14a506",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 12116,
                "upload_time": "2015-01-28T13:22:01",
                "url": "https://files.pythonhosted.org/packages/09/1e/ca6f2d5484be7e7814bac24fb6bdd2a8376d3683884c7a3dce35d2d802b0/intervaltree_bio-1.0.0.zip"
            }
        ],
        "1.0.1": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "aed813f69920e8f53fa8ce678256e226",
                    "sha256": "4f8ee8d5951c06072fdf03463bcd315920ef20b97947e85281330def79cdb2cd"
                },
                "downloads": -1,
                "filename": "intervaltree_bio-1.0.1.zip",
                "has_sig": false,
                "md5_digest": "aed813f69920e8f53fa8ce678256e226",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": null,
                "size": 12165,
                "upload_time": "2015-01-28T20:26:04",
                "url": "https://files.pythonhosted.org/packages/de/e6/c542057e7054cdb4139162041588d3b20f49dace223e7303a99a240bf6fd/intervaltree_bio-1.0.1.zip"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "aed813f69920e8f53fa8ce678256e226",
                "sha256": "4f8ee8d5951c06072fdf03463bcd315920ef20b97947e85281330def79cdb2cd"
            },
            "downloads": -1,
            "filename": "intervaltree_bio-1.0.1.zip",
            "has_sig": false,
            "md5_digest": "aed813f69920e8f53fa8ce678256e226",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": null,
            "size": 12165,
            "upload_time": "2015-01-28T20:26:04",
            "url": "https://files.pythonhosted.org/packages/de/e6/c542057e7054cdb4139162041588d3b20f49dace223e7303a99a240bf6fd/intervaltree_bio-1.0.1.zip"
        }
    ]
}