Metadata-Version: 1.1
Name: pygenome
Version: 1.0.0a18
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
        ========
        
        |Build Status|\ |Build status2|\ |CircleCI| |Coverage
        Status|\ |Documentation Status|
        
        Pygenome provide access to the `Saccharomyces
        cerevisiae <https://microbewiki.kenyon.edu/index.php/Saccharomyces_cerevisiae>`__
        genome from Python. `Genes <http://en.wikipedia.org/wiki/Gene>`__,
        `promoters <http://en.wikipedia.org/wiki/Promoter_(genetics)>`__,
        `terminators <http://en.wikipedia.org/wiki/Terminator_(genetics)>`__,
        and `intergenic <http://en.wikipedia.org/wiki/Intergenic_region>`__,
        sequences as well as the deletion
        `loci <http://en.wikipedia.org/wiki/Locus_(genetics)>`__ created by the
        `genome wide deletion
        project <http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html>`__
        are available by their systematic names (like
        `YPR080w <http://www.yeastgenome.org/locus/S000006284/overview>`__) or
        by standard name (like
        `CYC1 <http://www.yeastgenome.org/locus/S000003809/overview>`__). DNA
        sequences are returned as Biopython
        `SeqRecord <http://biopython.org/wiki/SeqRecord>`__ objects.
        
        Typical usage at the `IPython <http://ipython.org/>`__ command line
        could look like this:
        
        ::
        
            from pygenome import sg
        
            sg.gene["TEF1"]
            Out[2]: yeast gene YPR080W
        
            sg.gene["TEF1"].cds
            Out[3]: SeqRecord(seq=Seq('ATGGGTAAAGAGAAGTCTCACATTAACGTTGTCGTTATCGGTCATGTCGATTCT...TAA',
                    IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='BK006949 REGION: 700594..701970', dbxrefs=[])
        
            sg.gene["TEF1"].locus()
            Out[4]: SeqRecord(seq=Seq('CTTCATCGGTATCTTCGCTATATTCTTTTTAGTCGAATTTGCGGGGAGAAGATG...AAC',
                    IUPACAmbiguousDNA()), id='BK006949.2', name='BK006949', description='BK006949 REGION: 699594..702970', dbxrefs=[])
        
            sg.gene["TEF1"].promoter
            Out[5]: SeqRecord(seq=Seq('ACAATGCATACTTTGTACGTTCAAAATACAATGCAGTAGATATATTTATGCATA...AAA',
                    IUPACAmbiguousDNA()), id='YPR079W_YPR080W', name='.', description='BK006949 REGION: 700015..700593', dbxrefs=[])
        
            sg.gene["TEF1"].deletion_locus
            Out[6]: 'No deletion primers available!'
        
        
            Out[7]: SeqRecord(seq=Seq('GAGGCACCAGCGTCAGCATTTTCAAAGGTGTGTTCTTCGTCAGACATGTTTTAG...GTG',
                    IUPACAmbiguousDNA()), id='yjr048w::KanMX4 locus with 1000 bp up and 1000 bp downstream DNA',
                    name='yjr048w::KanMX4', description='<unknown description>', dbxrefs=[])
        
        +---------+--------------+-------------------------------------------------------+
        | ver     | date         | comment                                               |
        +=========+==============+=======================================================+
        | 1.0.0   | 2017-        | ?                                                     |
        +---------+--------------+-------------------------------------------------------+
        | 0.9.5   | 2017-01-01   | Python 3 release                                      |
        +---------+--------------+-------------------------------------------------------+
        | 0.9.0   | 2015-05-01   | Changed interface to a more object oriented style     |
        +---------+--------------+-------------------------------------------------------+
        | 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                                         |
        +---------+--------------+-------------------------------------------------------+
        
        Installation using conda on Anaconda
        ------------------------------------
        
        The absolutely best way of installing and using pygenome is to use the
        free `Anaconda <https://store.continuum.io/cshop/anaconda>`__ or
        `Miniconda <http://conda.pydata.org/miniconda.html>`__ python
        distributions.
        
        Anaconda is a large download (about 400 Mb) while Miniconda is about
        40-50 Mb.
        
        Once Anaconda (or Miniconda) is installed, the conda package manager can
        be used to install pygenome from the
        `BjornFJohansson <https://anaconda.org/bjornfjohansson>`__ package
        channel.
        
        The first step is to add the channel by typing the command below
        followed by return:
        
        ::
        
            conda config --append channels BjornFJohansson
        
        Then pygenome can be installed by typing the command below followed by
        return:
        
        ::
        
            conda install pygenome
        
        This works on Windows, MacOSX and Linux, and installs all necessary
        dependencies automatically.
        
        Requirements
        ------------
        
        -  `Python 3 <http://www.python.org>`__ (0.9.0 was the last to support
           Python 2.7.)
        -  `pydna <http://pypi.python.org/pypi/pydna>`__
        -  `requests <http://pypi.python.org/pypi/requests>`__
        -  `appdirs <https://pypi.python.org/pypi/appdirs>`__
        
        Install with pip
        ----------------
        
        The second best way of installing pygenome is by using
        `pip <https://packaging.python.org/en/latest/installing.html#installing-from-pypi>`__
        
        ::
        
            sudo pip install pygenome
        
        Source Code Repository
        ~~~~~~~~~~~~~~~~~~~~~~
        
        pydna source code is hosted on
        `Github <https://github.com/BjornFJohansson/pygenome>`__.
        
        .. |Build Status| image:: https://travis-ci.org/BjornFJohansson/pygenome.svg?branch=master
           :target: https://travis-ci.org/BjornFJohansson/pygenome
        .. |Build status2| image:: https://ci.appveyor.com/api/projects/status/aplxufiixw124dvr?svg=true
           :target: https://ci.appveyor.com/project/BjornFJohansson/pygenome
        .. |CircleCI| image:: https://circleci.com/gh/BjornFJohansson/pygenome.svg?style=svg
           :target: https://circleci.com/gh/BjornFJohansson/pygenome
        .. |Coverage Status| image:: https://coveralls.io/repos/github/BjornFJohansson/pygenome/badge.svg?branch=master
           :target: https://coveralls.io/github/BjornFJohansson/pygenome?branch=master
        .. |Documentation Status| image:: https://readthedocs.org/projects/pygenome/badge/?version=latest
           :target: http://pygenome.readthedocs.io/en/latest/?badge=latest
        
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 :: 3.5
Classifier: Topic :: Education
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
