Metadata-Version: 1.1
Name: pygenome
Version: 0.5.0
Summary: Accessing the Saccharomyces cerevisiae genome from Python
Home-page: http://pypi.python.org/pypi/pygenome/
Author: Björn Johansson
Author-email: bjorn_johansson@bio.uminho.pt
License: LICENSE.txt
Description: ========
        pygenome
        ========
        
        .. image:: https://travis-ci.org/BjornFJohansson/pygenome.svg 
            :target: https://travis-ci.org/BjornFJohansson/pygenome
            
        .. image:: https://coveralls.io/repos/BjornFJohansson/pygenome/badge.svg?branch=master 
            :target: https://coveralls.io/r/BjornFJohansson/pygenome?branch=master
          
        .. image:: https://readthedocs.org/projects/pygenome/badge/?version=latest
            :target: https://readthedocs.org/projects/pygenome/?badge=latest
            :alt: Documentation Status
        
        .. image:: https://pypip.in/download/pygenome/badge.svg
            :target: https://pypi.python.org/pypi/pygenome/
            :alt: Downloads
            
        .. image:: https://pypip.in/version/pygenome/badge.svg
            :target: https://pypi.python.org/pygenome/pydna/
            :alt: Latest Version
        
        .. image:: https://pypip.in/wheel/pydna/badge.svg
            :target: https://pypi.python.org/pypi/pydna/
            :alt: Wheel Status
        
        Pygenome provide a module for accessing the Saccharomyces cerevisiae genome from 
        Python. Genes, promoters, terminators and intergenic
        sequences are available by systematic names (like YPR080w) or by standard name.
        DNA sequences are returned as Biopython SeqRecord objects. Biopython, percache and
        appdirs are required for installation.
        
        Typical usage at the command line could look like this::
        
            >>> from pygenome import sg            
            >>> sg.locus("TEF1")
            SeqRecord(seq=Seq('CTTCATCGGTATCTTCGCTATATTCTTTTTAGTCGAATTTGCGGGGAGAAGATG...AAC', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='TPA: Saccharomyces cerevisiae S288c chromosome XVI.', dbxrefs=[])
            >>> sg.locus("YPR080w")
            SeqRecord(seq=Seq('CTTCATCGGTATCTTCGCTATATTCTTTTTAGTCGAATTTGCGGGGAGAAGATG...AAC', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='TPA: Saccharomyces cerevisiae S288c chromosome XVI.', dbxrefs=[])
            >>> a=sg.locus("TEF1")
            >>> b=sg.locus("YPR080w")
            >>> str(a.seq) == str(b.seq)
            True
            >>> prom=sg.promoter("TEF1")
            >>> prom
            SeqRecord(seq=Seq('ACAATGCATACTTTGTACGTTCAAAATACAATGCAGTAGATATATTTATGCATA...AAA', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='TPA: Saccharomyces cerevisiae S288c chromosome XVI.', dbxrefs=[])
            >>> term=sg.terminator("TEF1")
            >>> term
            SeqRecord(seq=Seq('GGAGATTGATAAGACTTTTCTAGTTGCATATCTTTTATATTTAAATCTTATCTA...CAG', IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='TPA: Saccharomyces cerevisiae S288c chromosome XVI.', dbxrefs=[])
            
            
        NEWS
        ====
        
        
        =======   ========== =============================================================
        version   date       comment
        =======   ========== =============================================================
        0.5.0     2015-03-03 Documentation, automatic build,test and deployment
        
        0.0.6     2014-06-17 Bugfix
        
        0.0.5     2014-06-14 Simpler api (see example above)
        
        0.0.1     2013-08-01 first release
        =======   ========== =============================================================
        
        
        System Requirements
        ===================
        
        - `Python 2.7 <http://www.python.org>`_.
        
        - `biopython <http://pypi.python.org/pypi/biopython>`_.
        
        - `percache  <http://pypi.python.org/pypi/percache>`_.
        
        - `appdirs <http://pypi.python.org/pypi/appdirs>`_.
        
        Python 2.x
        ----------
        
        Versions other than 2.7 has not been tried with this software.
        Version 2.7.3 was used to build the distribution.
        
        Python 3.x
        ----------
        
        This code has not been tested with python 3.
        
        Installation
        ============
        
        Source
        ------
        
        Open the pydna source code directory (containing the setup.py file) in
        terminal and type:
        
            sudo python setup.py install <enter>
        
        If you need to do additional configuration, e.g. changing the base
        directory, please type `python setup.py`, or see the documentation for
        Setuptools.
        
        
        Source Code Repository
        ----------------------
        
        pydna source code is hosted on Github:
        
        https://github.com/BjornFJohansson/pygenome
        
        
        Distribution Structure
        ======================
        
        README.rst          -- This file.
        
        LICENSE.txt         -- What you can do with the code.
        
        MANIFEST.in         -- Tells distutils what files to distribute
        
        setup.py            -- Installation file.
        
        pygenome/           -- The actual code.
        
        docs/               -- Documentation.
        
        scripts/            -- Miscellaneous perhaps useful scripts
        
        tests/              -- Testing code
        
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
Classifier: Environment :: Console
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Education
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
