{
    "info": {
        "author": "Bj\u00f6rn Johansson",
        "author_email": "bjorn_johansson@bio.uminho.pt",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Environment :: Console",
            "Intended Audience :: Education",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: BSD License",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Topic :: Education",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "# [![icon](SuperYeast.jpg)](http://www.yeastgenome.org/) [pygenome](https://pypi.python.org/pypi/pygenome)\n\n[![Build Status](https://travis-ci.org/BjornFJohansson/pygenome.svg?branch=master)](https://travis-ci.org/BjornFJohansson/pygenome)\n[![Build status2](https://ci.appveyor.com/api/projects/status/aplxufiixw124dvr?svg=true)](https://ci.appveyor.com/project/BjornFJohansson/pygenome)\n[![Codeship Status for BjornFJohansson/pygenome](https://app.codeship.com/projects/9ff45010-5b6d-0137-5291-36b827d8f51b/status?branch=master)](https://app.codeship.com/projects/342668)\n[![codecov](https://codecov.io/gh/BjornFJohansson/pygenome/branch/master/graph/badge.svg)](https://codecov.io/gh/BjornFJohansson/pygenome)\n[![Documentation Status](https://readthedocs.org/projects/pygenome/badge/?version=latest)](http://pygenome.readthedocs.io/en/latest/?badge=latest)\n[![PyPI version](https://badge.fury.io/py/pygenome.svg)](https://badge.fury.io/py/pygenome)\n[![Anaconda-Server Badge](https://anaconda.org/bjornfjohansson/pygenome/badges/version.svg)](https://anaconda.org/bjornfjohansson/pygenome)\n\nHarness the awesome power of yeast genetics through python! Pygenome provide access to the [Saccharomyces cerevisiae](https://microbewiki.kenyon.edu/index.php/Saccharomyces_cerevisiae)\ngenome from Python. [Genes](http://en.wikipedia.org/wiki/Gene),\n[promoters](http://en.wikipedia.org/wiki/Promoter_(genetics)),\n[terminators](http://en.wikipedia.org/wiki/Terminator_(genetics)), and\n[intergenic](http://en.wikipedia.org/wiki/Intergenic_region), sequences\nas well as the deletion [loci](http://en.wikipedia.org/wiki/Locus_(genetics)) created by the\n[genome wide deletion project](http://www-sequence.stanford.edu/group/yeast_deletion_project/deletions3.html)\nare available by their systematic names (like [YPR080w](http://www.yeastgenome.org/locus/S000006284/overview)) or by\nstandard name (like [CYC1](http://www.yeastgenome.org/locus/S000003809/overview)). DNA\nsequences are returned as Biopython\n[SeqRecord](http://biopython.org/wiki/SeqRecord) objects. Thanks to [SGD](http://www.yeastgenome.org/) for letting me use the SuperYeast logotype above.\n\nTypical usage at the [IPython](http://ipython.org/) command line could look like this:\n\n    from pygenome import sg\n\n    mygene = sg.stdgene[\"XKS1\"]\n\n    mygene\n    Out[3]: Gene XKS1/YGR194C\n\n    mygene.short_description\n    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\n\n    sg.sysgene[\"YGR194C\"]\n    Out[5]: Gene XKS1/YGR194C\n\n    mygene.cds\n    Out[6]: SeqRecord(seq=Seq('ATGTTGTGTTCAGTAATTCAGAGACAGACAAGAGAGGTTTCCAACACAATGTCT...TAA', IUPACAmbiguousDNA()), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(887876..886072)', dbxrefs=[])\n\n    mygene.locus()\n    Out[7]: SeqRecord(seq=Seq('ATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATATGTTAA...GAA', IUPACAmbiguousDNA()), id='BK006941.2', name='BK006941', description='BK006941 REGION: complement(888876..885072)', dbxrefs=[])\n\n    mygene.promoter\n    Out[8]: SeqRecord(seq=Seq('ATGATGATCCTGCTGTAGTTATGGCACTAAAGTTTTTTTGTAAATCTTTTTATA...TTA', IUPACAmbiguousDNA()), id='YGR195W_YGR194C', name='.', description='BK006941.2 REGION: complement(887876..888881)', dbxrefs=[])\n\n    mygene.terminator\n    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=[])\n\n    mygene.downstream_gene\n    Out[10]: Gene PDX1/YGR193C\n\n    mygene.upstream_gene\n    Out[11]: Gene SKI6/YGR195W\n\n    mygene.deletion_locus\n    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=[])\n\n\nhttp://www-sequence.stanford.edu/group/yeast_deletion_project/downloads.html\n\n| ver   | date       | comment                                             |\n|-------|------------|-----------------------------------------------------|\n| 2.0.0 | 2017-09-02 | split sg.gene dict into sg.stdgene and sg.sysgene   |\n| 1.0.0 | 2017-03-24 | Internal stuff, automativ build & test              |\n| 0.9.5 | 2017-01-01 | Python 3 release                                    |\n| 0.9.0 | 2015-05-01 | Changed interface to a more object oriented style   |\n| 0.5.0 | 2015-03-03 | Documentation, automatic build, test and deployment |\n| 0.0.6 | 2014-06-17 | Bugfix                                              |\n| 0.0.5 | 2014-06-14 | Simpler api (see example above)                     |\n| 0.0.1 | 2013-08-01 | first release                                       |\n\n## Installation using conda on Anaconda\n\nThe absolutely best way of installing and using pygenome is to use the \nfree [Anaconda](https://store.continuum.io/cshop/anaconda) or [Miniconda](http://conda.pydata.org/miniconda.html) python distributions.\n\nAnaconda is a large download (about 400 Mb) while Miniconda is about 40-50 Mb. \n\nOnce Anaconda (or Miniconda) is installed, the conda package manager can be used to install pygenome \nfrom the [BjornFJohansson](https://anaconda.org/bjornfjohansson) package channel.\n\nThe first step is to add the channel by typing the command below followed by return:\n\n    conda config --append channels BjornFJohansson\n\nThen pygenome can be installed by typing the command below followed by return:\n\n    conda install pygenome\n\nThis works on Windows, MacOSX and Linux, and installs all necessary dependencies automatically.\n\n## Requirements\n\n- [Python 3.6 or 3.7](http://www.python.org) (pygenome version 0.9.0 was the last to support Python 2.7.)\n- [pydna](http://pypi.python.org/pypi/pydna)\n- [requests](http://pypi.python.org/pypi/requests)\n- [appdirs](https://pypi.python.org/pypi/appdirs)\n\n## Install with pip\n\nThe second best way of installing pygenome is by using\n[pip](https://packaging.python.org/en/latest/installing.html#installing-from-pypi)\n\n    sudo pip install pygenome\n\n### Source Code Repository\n\npydna source code is hosted on [Github](https://github.com/BjornFJohansson/pygenome).\n\n\n",
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