Metadata-Version: 1.1
Name: pyliftover
Version: 0.3
Summary: Pure-python implementation of UCSC ``liftOver`` genome coordinate conversion.
Home-page: https://github.com/konstantint/pyliftover
Author: Konstantin Tretyakov
Author-email: kt@ut.ee
License: MIT
Description: ============================================================================
        Pure-python implementation of UCSC ``liftOver`` genome coordinate conversion
        ============================================================================
        
        .. image:: https://travis-ci.org/konstantint/pyliftover.png?branch=master   :target: https://travis-ci.org/konstantint/pyliftover
        
        PyLiftover is a library for quick and easy conversion of genomic (point) coordinates between different assemblies.
        
        It uses the same logic and coordinate conversion mappings as the UCSC `liftOver tool <http://genome.ucsc.edu/cgi-bin/hgLiftOver>`_.
        
        As of current version (0.2), PyLiftover only does conversion of point coordinates, that is, 
        unlike ``liftOver``, it does not convert ranges, nor does it provide any special facilities to work with BED files.
        For single-point coordinates it produces exactly the same output as ``liftOver`` (verified with at least the ``hg17ToHg18.over.chain.gz`` file for now).
        
        Installation
        ------------
        
        The simplest way to install the package is via ``easy_install`` or ``pip``::
        
            $ easy_install pyliftover
        
        Usage
        -----
        The primary usage example, supported by the library is the following::
        
            from pyliftover import LiftOver
            lo = LiftOver('hg17', 'hg18')
            lo.convert_coordinate('chr1', 1000000)
        
        The first line will automatically download the hg17-to-hg18 coordinate conversion `chain file <http://genome.ucsc.edu/goldenPath/help/chain.html>`_ from UCSC,
        unless it is already cached or available in the current directory. Alternatively, you may provide your own chain file::
        
            lo = LiftOver('hg17ToHg18.over.chain.gz')
            lo.convert_coordinate('chr1', 1000000, '-')
        
        The result of ``lo.convert_coordinate`` call is either ``None`` (if the source chromosome name is unrecognized) or a list of target positions in the
        new assembly. The list may be empty (locus is deleted in the new assembly), have a single element (locus matched uniquely), or, in principle, 
        have multiple elements (although this is probably a rare occasion for most default intra-species genomic conversions).
        Note that coordinates in the tool are 0-based. That is, a position that you would refer to in the genome browser by ``chr1:10`` 
        corresponds to coordinate ``9`` in PyLiftover's terms.
        
        Although you may try to apply the tool with arbitrary chain files, like the original ``liftOver`` tool, it makes most sense for conversion of 
        coordinates between different assemblies of the same species.
        
        
        See also
        --------
        
        * Blog post: http://fouryears.eu/2013/02/25/the-curse-of-genomic-coordinates/
        * Report issues and submit fixes at Github: https://github.com/konstantint/pyliftover
        
Keywords: bioinformatics liftover genome-analysis
Platform: Platform Independent
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 2
Classifier: Programming Language :: Python :: 3
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
