Metadata-Version: 1.1
Name: pygenome
Version: 2.0.0
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-Content-Type: UNKNOWN
Description: # [![icon](SuperYeast.jpg)](http://www.yeastgenome.org/) [pygenome](https://pypi.python.org/pypi/pygenome)
        
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        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).
        
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
