Metadata-Version: 1.1
Name: pygenome
Version: 0.9.5
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://badge.fury.io/py/pygenome.svg
            :target: http://badge.fury.io/py/pygenome
        
        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!'
        
             sg.gene["CYC1"].deletion_locus()
            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=[])
        
        
        
        
        =======   ========== =============================================================
        version   date       comment
        =======   ========== =============================================================
        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
        =======   ========== =============================================================
        
        
        System Requirements
        ===================
        
        - `Python 3.5 <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 2.7
        ----------
        
        Version 0.9.0 was the last one to support Python 2.7.
        
        Installation
        ============
        
        Source
        ------
        
        The 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
        
        
        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 :: 3.5
Classifier: Topic :: Education
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
