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        "author": "Konstantin Tretyakov",
        "author_email": "kt@ut.ee",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 5 - Production/Stable",
            "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"
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        "description": "============================================================================\nPure-python implementation of UCSC ``liftOver`` genome coordinate conversion\n============================================================================\n\n.. image:: https://travis-ci.org/konstantint/pyliftover.png?branch=master   :target: https://travis-ci.org/konstantint/pyliftover\n\nPyLiftover is a library for quick and easy conversion of genomic (point) coordinates between different assemblies.\n\nIt uses the same logic and coordinate conversion mappings as the UCSC `liftOver tool <http://genome.ucsc.edu/cgi-bin/hgLiftOver>`_.\n\nAs of current version (0.2), PyLiftover only does conversion of point coordinates, that is, \nunlike ``liftOver``, it does not convert ranges, nor does it provide any special facilities to work with BED files.\nFor single-point coordinates it produces exactly the same output as ``liftOver`` (verified with at least the ``hg17ToHg18.over.chain.gz`` file for now).\n\nInstallation\n------------\n\nThe simplest way to install the package is via ``easy_install`` or ``pip``::\n\n    $ easy_install pyliftover\n\nUsage\n-----\nThe primary usage example, supported by the library is the following::\n\n    from pyliftover import LiftOver\n    lo = LiftOver('hg17', 'hg18')\n    lo.convert_coordinate('chr1', 1000000)\n\nThe first line will automatically download the hg17-to-hg18 coordinate conversion `chain file <http://genome.ucsc.edu/goldenPath/help/chain.html>`_ from UCSC,\nunless it is already cached or available in the current directory. Alternatively, you may provide your own chain file::\n\n    lo = LiftOver('hg17ToHg18.over.chain.gz')\n    lo.convert_coordinate('chr1', 1000000, '-')\n\nThe result of ``lo.convert_coordinate`` call is either ``None`` (if the source chromosome name is unrecognized) or a list of target positions in the\nnew assembly. The list may be empty (locus is deleted in the new assembly), have a single element (locus matched uniquely), or, in principle, \nhave multiple elements (although this is probably a rare occasion for most default intra-species genomic conversions).\nNote that coordinates in the tool are 0-based. That is, a position that you would refer to in the genome browser by ``chr1:10`` \ncorresponds to coordinate ``9`` in PyLiftover's terms.\n\nAlthough you may try to apply the tool with arbitrary chain files, like the original ``liftOver`` tool, it makes most sense for conversion of \ncoordinates between different assemblies of the same species.\n\n\nSee also\n--------\n\n* Blog post: http://fouryears.eu/2013/02/25/the-curse-of-genomic-coordinates/\n* Report issues and submit fixes at Github: https://github.com/konstantint/pyliftover",
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        "keywords": "bioinformatics liftover genome-analysis",
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