{
    "info": {
        "author": "Konstantin Tretyakov",
        "author_email": "kt@ut.ee",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: MIT License",
            "Operating System :: OS Independent",
            "Programming Language :: Python :: 2",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
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        "description": "==============================================\nSimple access to the reference genomes at UCSC\n==============================================\n\nThe package allows to easily download and use genomic data at UCSC.\nThis is essentially a thin \"caching\" wrapper around the ``twobitreader`` library.\n\nInstallation\n------------\n\nThe simplest way to install the package is via ``easy_install`` or ``pip``::\n\n    $ easy_install ucscgenome\n\nDependencies\n------------\n\n- ``twobitreader``\n\nUsage\n-----\nThe primary usage example is the following::\n\n   from ucscgenome import Genome\n   g = Genome('sacCer2')\n   print str(g['chrI'][0:100])\n\nOn the second line of the above example the following steps are performed:\n\n* The local ``cache directory`` is searched for the pre-downloaded genome data. If the data is readily available, it is opened for reading.\n* If there is not cached version of the ``sacCer2`` genome, it is downloaded from the UCSC site to the cache directory.\n* The local data is downloaded and stored using the compact `2bit <http://www.its.caltech.edu/~alok/reviews/blatSpecs.html>`_ format.\n\nYou can configure the details of the procedure by providing additional options to the ``Genome`` constructor::\n\n   g = Genome('hg19', cache_dir='my_genomes', use_web=False)\n   \nwhich means that the genome data is to be searched for in the ``./my_genomes`` directory and in no case should a download be attempted, or::\n\n   g = Genome('hg19', source_url_pattern='http://my.site.com/genomes/%(id)s/%(id)s.2bit')\n\nwhich means that the genomic data is to be downloaded from your own server rather than UCSD's.\n\nSee also\n--------\n\n* Report issues and submit fixes at Github: https://github.com/konstantint/ucscgenome\n\nRelated packages\n----------------\n\n* http://pyucsc.readthedocs.org/\n* https://pypi.python.org/pypi/twobitreader\n* https://pypi.python.org/pypi/pyfasta\n* https://pypi.python.org/pypi/cruzdb\n* https://pypi.python.org/pypi/pyliftover",
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        "keywords": "bioinformatics ucsc data-access genome-analysis",
        "license": "MIT",
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        "name": "ucscgenome",
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