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        "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",
            "Programming Language :: Python :: 3",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "=====================================================================================\nSQLAlchemy-based interface to the oPOSSUM3 transcription factor binding site database\n=====================================================================================\n\n.. image:: https://travis-ci.org/konstantint/pyopossum3.png?branch=master   :target: https://travis-ci.org/konstantint/pyopossum3\n\nThe package provides an object-oriented access interface to the `oPOSSUM3 <http://opossum.cisreg.ca/oPOSSUM3/>`_ raw database tables.\n\nInstallation\n------------\n\nThe simplest way to install the package is via ``easy_install`` or ``pip``::\n\n    $ easy_install pyopossum3\n\nDependencies\n------------\n\n- ``SQLAlchemy``\n- ``PyMySQL`` or any other `SQLAlchemy-compatible MySQL connector <http://docs.sqlalchemy.org/en/rel_0_9/dialects/mysql.html>`_.\n\nUsage\n-----\nA usage example is the following::\n\n   >>> from pyopossum3 import Opossum\n   >>> o = Opossum(\"mysql+pymysql://opossum_r:@opossum.cmmt.ubc.ca/oPOSSUM3_human\")\n   >>> o.ConservedTfbs.query.first().gene\n   >>> o.ExternalGeneId.query.filter(o.ExternalGeneId.external_id.in_(['TSPAN6'])).filter(o.ExternalGeneId.gene.has(chr='X')).first().gene\n   ... etc ...\n\nThe second line creates a connection to the oPOSSUM server, and the third/fourth query the ``conserved_tfbss`` and ``external_gene_ids`` tables using SQLAlchemy syntax.\n\nNaturally, for heavy analyses, you are suggested to set up your own copy of the database.\nSee `here <http://opossum.cisreg.ca/oPOSSUM3/download.html>`_ for instructions on how to download the data.\n\nYou can get a feeling for the structure of the database by running the following::\n\n    >>> for cls in o.all_orm_classes:\n    >>>    print cls.query.first()\n\nThe main table you should probably care about is ``ConservedTfbs``, which contains matches in the vicinity of each gene, annotated with match score and conservation level.\n\nAn example using the ``ucscgenome`` package to verify that TFBS sequences are indeed correct::\n    \n    >>> c = o.ConservedTfbs.query.filter(o.ConservedTfbs.strand==1).first()\n    >>> c.gene.chr, c.absolute_start, c.absolute_end, c.seq\n    ('X', 99890235L, 99890253L, 'AGAAACATTGCATACTGC')\n    >>> from ucscgenome import Genome\n    >>> g = Genome('hg19')\n    >>> g['chrX'][99890235:99890253]\n    'AGAAACATTGCATACTGC'\n\nNote\n----\nThe author of this package is not associated with the creators and maintainers of the oPOSSUM3 tool.\n\nSee also\n--------\n\n* Report issues and submit fixes at Github: https://github.com/konstantint/pyopossum3",
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        "keywords": "bioinformatics oPOSSUM3 data-access transcription tfbs",
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