Metadata-Version: 1.1
Name: ucscgenome
Version: 0.1
Summary: Simple access to the reference genomes at UCSC
Home-page: https://github.com/konstantint/ucscgenome
Author: Konstantin Tretyakov
Author-email: kt@ut.ee
License: MIT
Description: ==============================================
        Simple access to the reference genomes at UCSC
        ==============================================
        
        The package allows to easily download and use genomic data at UCSC.
        This is essentially a thin "caching" wrapper around the ``twobitreader`` library.
        
        Installation
        ------------
        
        The simplest way to install the package is via ``easy_install`` or ``pip``::
        
            $ easy_install ucscgenome
        
        Dependencies
        ------------
        
        - ``twobitreader``
        
        Usage
        -----
        The primary usage example is the following::
        
           from ucscgenome import Genome
           g = Genome('sacCer2')
           print str(g['chrI'][0:100])
        
        On the second line of the above example the following steps are performed:
        
        * The local ``cache directory`` is searched for the pre-downloaded genome data. If the data is readily available, it is opened for reading.
        * If there is not cached version of the ``sacCer2`` genome, it is downloaded from the UCSC site to the cache directory.
        * The local data is downloaded and stored using the compact `2bit <http://www.its.caltech.edu/~alok/reviews/blatSpecs.html>`_ format.
        
        You can configure the details of the procedure by providing additional options to the ``Genome`` constructor::
        
           g = Genome('hg19', cache_dir='my_genomes', use_web=False)
           
        which 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::
        
           g = Genome('hg19', source_url_pattern='http://my.site.com/genomes/%(id)s/%(id)s.2bit')
        
        which means that the genomic data is to be downloaded from your own server rather than UCSD's.
        
        See also
        --------
        
        * Report issues and submit fixes at Github: https://github.com/konstantint/ucscgenome
        
        Related packages
        ----------------
        
        * http://pyucsc.readthedocs.org/
        * https://pypi.python.org/pypi/twobitreader
        * https://pypi.python.org/pypi/pyfasta
        * https://pypi.python.org/pypi/cruzdb
        * https://pypi.python.org/pypi/pyliftover
        
Keywords: bioinformatics ucsc data-access 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: Topic :: Scientific/Engineering :: Bio-Informatics
