Metadata-Version: 1.1
Name: pygenome
Version: 1.0.2
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-Content-Type: UNKNOWN
Description: 
        |icon| `pygenome <https://pypi.python.org/pypi/pygenome>`__
        ===========================================================
        
        |Build Status| |Build status2|\ |Codeship Status for
        BjornFJohansson/pygenome| |codecov| |Documentation Status|\ |PyPI
        version| |Anaconda-Server Badge|
        
        Harness the awesome power of yeast genetics through python! 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. Thanks to
        `SGD <http://www.yeastgenome.org/>`__ for letting me use the SuperYeast
        logotype above.
        
        Typical usage at the `IPython <http://ipython.org/>`__ command line
        could look like this:
        
        ::
        
            from pygenome import sg
        
            mygene = sg.stdgene["XKS1"]
        
            mygene
            Out[3]: Gene XKS1/YGR194C
        
            mygene.short_description
            Out[4]: Xylulokinase; converts D-xylulose and ATP to xylulose 5-phosphate and ADP; rate limiting step in fermentation of xylulose; required for xylose fermentation by recombinant S. cerevisiae strains
        
            sg.sysgene["YGR194C"]
            Out[5]: Gene XKS1/YGR194C
        
            mygene.cds
            Out[6]: SeqRecord(seq=Seq('ATGTTGTGTTCAGTAATTCAGAGACAGACAAGAGAGGTTTCCAACACAATGTCT...TAA', IUPACAmbiguousDNA()), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(887876..886072)', dbxrefs=[])
        
            mygene.locus()
            Out[7]: SeqRecord(seq=Seq('ATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATATGTTAA...GAA', IUPACAmbiguousDNA()), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(888876..885072)', dbxrefs=[])
        
            mygene.promoter
            Out[8]: SeqRecord(seq=Seq('ATGATGATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATA...TTA', IUPACAmbiguousDNA()), id='YGR195W_YGR194C', name='.', description='BK006941.2 REGION: complement(887876..888881)', dbxrefs=[])
        
            mygene.terminator
            Out[9]: SeqRecord(seq=Seq('AATATGTTTGAATAATTTATCATGCCCTGACAAGTACACACAAACACAGACACA...AAA', IUPACAmbiguousDNA()), id='YGR194C_YGR195W', name='.', description='Intergenic sequence between upstream gene YGR194C and downstream gene Gene PDX1/YGR193C', dbxrefs=[])
        
            mygene.downstream_gene
            Out[10]: Gene PDX1/YGR193C
        
            mygene.upstream_gene
            Out[11]: Gene SKI6/YGR195W
        
            mygene.deletion_locus
            Out[12]: SeqRecord(seq=Seq('ATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATATGTTAA...GAA', IUPACAmbiguousDNA()), id='ygr194c::KanMX4 locus with 1000 bp up and 1000 bp downstream DNA', name='ygr194c::KanMX4', description='description?', dbxrefs=[])
        
        +---------+--------------+-------------------------------------------------------+
        | ver     | date         | comment                                               |
        +=========+==============+=======================================================+
        | 2.0.0   | 2017-09-02   | split sg.gene dict into sg.stdgene and sg.sysgene     |
        +---------+--------------+-------------------------------------------------------+
        | 1.0.0   | 2017-03-24   | Internal stuff, automativ build & test                |
        +---------+--------------+-------------------------------------------------------+
        | 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 3.5 or 3.6 <http://www.python.org>`__ (pygenome version 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>`__.
        
        .. |icon| image:: SuperYeast.jpg
           :target: http://www.yeastgenome.org/
        .. |Build Status| image:: https://travis-ci.org/BjornFJohansson/pygenome.svg?branch=master
           :target: https://travis-ci.org/BjornFJohansson/pygenome
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           :target: https://ci.appveyor.com/project/BjornFJohansson/pygenome
        .. |Codeship Status for BjornFJohansson/pygenome| image:: https://app.codeship.com/projects/f461d290-71e3-0135-828b-52ef08dd0262/status?branch=master
           :target: https://app.codeship.com/projects/243478
        .. |codecov| image:: https://codecov.io/gh/BjornFJohansson/pygenome/branch/master/graph/badge.svg
           :target: https://codecov.io/gh/BjornFJohansson/pygenome
        .. |Documentation Status| image:: https://readthedocs.org/projects/pygenome/badge/?version=latest
           :target: http://pygenome.readthedocs.io/en/latest/?badge=latest
        .. |PyPI version| image:: https://badge.fury.io/py/pygenome.svg
           :target: https://badge.fury.io/py/pygenome
        .. |Anaconda-Server Badge| image:: https://anaconda.org/bjornfjohansson/pygenome/badges/version.svg
           :target: https://anaconda.org/bjornfjohansson/pygenome
        
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: Programming Language :: Python :: 3.6
Classifier: Topic :: Education
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
