{
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        "author": "The Biopython Contributors",
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            "Development Status :: 5 - Production/Stable",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: Freely Distributable",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: 3.6",
            "Topic :: Scientific/Engineering",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Python Modules"
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        "description": ".. image:: https://img.shields.io/pypi/v/biopython.svg\n   :alt: Biopython on the Python Package Index (PyPI)\n   :target: https://pypi.python.org/pypi/biopython\n.. image:: https://img.shields.io/conda/vn/conda-forge/biopython.svg\n   :alt: Biopython on the Conda package conda-forge channel\n   :target: https://anaconda.org/conda-forge/biopython\n.. image:: https://img.shields.io/travis/biopython/biopython/master.svg?logo=travis\n   :alt: Linux testing with TravisCI\n   :target: https://travis-ci.org/biopython/biopython/branches\n.. image:: https://img.shields.io/appveyor/ci/biopython/biopython/master.svg?logo=appveyor\n   :alt: Windows testing with AppVeyor\n   :target: https://ci.appveyor.com/project/biopython/biopython/history\n.. image:: https://img.shields.io/codecov/c/github/biopython/biopython/master.svg\n   :alt: TravisCI test coverage\n   :target: https://codecov.io/github/biopython/biopython/\n.. image:: http://depsy.org/api/package/pypi/biopython/badge.svg\n   :alt: Research software impact on Depsy\n   :target: http://depsy.org/package/python/biopython\n\n.. image:: https://github.com/biopython/biopython/raw/master/Doc/images/biopython_logo_m.png\n   :alt: The Biopython Project\n   :target: http://biopython.org\n\nBiopython README file\n=====================\n\nThe Biopython Project is an international association of developers of freely\navailable Python tools for computational molecular biology.\n\nOur user-centric documentation is hosted on http://biopython.org including\nthe main Biopython Tutorial and Cookbook:\n\n* HTML - http://biopython.org/DIST/docs/tutorial/Tutorial.html\n* PDF - http://biopython.org/DIST/docs/tutorial/Tutorial.pdf\n\nThis README file is intended primarily for people interested in working\nwith the Biopython source code, either one of the releases from the\nhttp://biopython.org website, or from our repository on GitHub\nhttps://github.com/biopython/biopython\n\nThe `NEWS <https://github.com/biopython/biopython/blob/master/NEWS.rst>`_\nfile summarises the changes in each release of Biopython.\n\nThe Biopython package is open source software made available under generous\nterms. Please see the `LICENSE\n<https://github.com/biopython/biopython/blob/master/LICENSE.rst>`_ file for\nfurther details.\n\nIf you use Biopython in work contributing to a scientific publication, we ask\nthat you cite our application note (below) or one of the module specific\npublications (listed on our website):\n\nCock, P.J.A. et al. Biopython: freely available Python tools for computational\nmolecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3\nhttp://dx.doi.org/10.1093/bioinformatics/btp163 pmid:19304878\n\n\nFor the impatient\n=================\n\nPython 2.7.9 onwards, and Python 3.4 onwards, include the package management\nsystem \"pip\" which should allow you to install Biopython (and its dependency\nNumPy if needed), upgrade or uninstall with just one terminal command::\n\n    pip install biopython\n    pip install --upgrade biopython\n    pip uninstall biopython\n\nSince Biopython 1.70 we have provided pre-compiled binary wheel packages on\nPyPI for Linux, Mac OS X and Windows. This means pip install should be quick,\nand not require a compiler.\n\nAs a developer or potential contributor, you may wish to download, build and\ninstall Biopython yourself. This is described below.\n\n\nPython Requirements\n===================\n\nWe currently recommend using Python 3.7 from http://www.python.org\n\nBiopython is currently supported and tested on the following Python\nimplementations:\n\n- Python 2.7, 3.4, 3.5, 3.6, 3.7 -- see http://www.python.org\n\n  Python 3 is the primary development platform for Biopython. We will drop\n  support for Python 2.7 no later than 2020, in line with the end-of-life or\n  sunset date for Python 2.7 itself.\n\n- PyPy2.7 v6.0.0, or PyPy3.5 v6.0.0 -- see http://www.pypy.org\n\n  Aside from ``Bio.trie`` (which does not compile as ``marshal.h`` is\n  currently missing under PyPy), everything should work. Older versions\n  of PyPy mostly work too.\n\n- Jython 2.7 -- see http://www.jython.org\n\n  We have decided to deprecate support for Jython, but aside from\n  ``Bio.Restriction``, modules with C code, or dependent on SQLite3 or NumPy,\n  everything should work. There are some known issues with test failures\n  which have not yet been resolved.\n\nBiopython 1.68 was our final release to support Python 2.6.\n\n\nOptional Dependencies\n=====================\n\nBiopython requires NumPy (see http://www.numpy.org) which will be installed\nautomatically if you install Biopython with pip (see below for compiling\nBiopython yourself).\n\nDepending on which parts of Biopython you plan to use, there are a number of\nother optional Python dependencies, which can be installed later if needed:\n\n- ReportLab, see http://www.reportlab.com/opensource/ (optional)\n  This package is only used in ``Bio.Graphics``, so if you do not need this\n  functionality, you will not need to install this package.\n\n- matplotlib, see http://matplotlib.org/ (optional)\n  ``Bio.Phylo`` uses this package to plot phylogenetic trees.\n\n- networkx, see http://networkx.lanl.gov/ (optional) and\n  pygraphviz or pydot, see http://networkx.lanl.gov/pygraphviz/ and\n  http://code.google.com/p/pydot/ (optional)\n  These packages are used for certain niche functions in ``Bio.Phylo``.\n\n- rdflib, see https://github.com/RDFLib/rdflib (optional)\n  This package is used in the CDAO parser under ``Bio.Phylo``.\n\n- psycopg2, see http://initd.org/psycopg/ (optional) or\n  PyGreSQL (pgdb), see http://www.pygresql.org/ (optional)\n  These packages are used by ``BioSQL`` to access a PostgreSQL database.\n\n- MySQL Connector/Python, see http://dev.mysql.com/downloads/connector/python/\n  This package is used by ``BioSQL`` to access a MySQL database, and is\n  supported on Python 2 and 3 and PyPy too.\n\n- mysqlclient, see https://github.com/PyMySQL/mysqlclient-python (optional)\n  This is a fork of the older MySQLdb and is used by ``BioSQL`` to access a\n  MySQL database. It is supported by Python 2.7, Python 3.5 and above, PyPy 2,\n  and PyPy 3.\n\nNote that some of these libraries are not available for PyPy or Jython,\nand not all are available for Python 3 yet either.\n\nIn addition there are a number of useful third party tools you may wish to\ninstall such as standalone NCBI BLAST, EMBOSS or ClustalW.\n\n\nInstallation From Source\n========================\n\nWe recommend using the pre-compiled binary wheels available on PyPI using::\n\n    pip install biopython\n\nHowever, if you need to compile Biopython yourself, the following are\nrequired at compile time - unless you are using Jython (support for which is\ndeprecated).\n\n- Python including development header files like ``python.h``, which on Linux\n  are often not installed by default (trying looking for and installing a\n  package named ``python-dev`` or ``python-devel`` as well as the ``python``\n  pacakge).\n\n- Appropriate C compiler for your version of Python, for example GCC on Linux,\n  MSVC on Windows. For Mac OS X, or as it is now branded, macOS, use Apple's\n  command line tools, which can be installed with the terminal command::\n\n      xcode-select --install\n\n  This will offer to install Apple's XCode development suite - you can, but it\n  is not needed and takes a lot of disk space.\n\nThen either download and decompress our source code, or fetch it using git.\nNow change directory to the Biopython source code folder and run::\n\n    python setup.py build\n    python setup.py test\n    sudo python setup.py install\n\nSubstitute ``python`` with your specific version, for example ``python3``,\n``pypy`` or ``jython``.\n\nTo exlude tests that require an internet connection (and which may take a long\ntime), use the ``--offline`` option::\n\n    python setup.py test --offline\n\nIf you need to do additional configuration, e.g. changing\nthe install directory prefix, please type ``python setup.py``, or see the\ndocumentation here:\n\n* HTML - http://biopython.org/DIST/docs/install/Installation.html\n* PDF - http://biopython.org/DIST/docs/install/Installation.pdf\n\n\nTesting\n=======\n\nBiopython includes a suite of regression tests to check if everything is\nrunning correctly. To run the tests, go to the biopython source code\ndirectory and type::\n\n    python setup.py build\n    python setup.py test\n\nIf you want to skip the online tests (which is recommended when doing repeated\ntesting), use::\n\n    python setup.py test --offline\n\nDo not panic if you see messages warning of skipped tests::\n\n    test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.\n\nThis most likely means that a package is not installed.  You can\nignore this if it occurs in the tests for a module that you were not\nplanning on using.  If you did want to use that module, please install\nthe required dependency and re-run the tests.\n\nSome of the tests may fail due to network issues, this is often down to\nchance or a service outage. If the problem does not go away on\nre-running the tests, you can use the ``--offline`` option.\n\nThere is more testing information in the Biopython Tutorial & Cookbook.\n\n\nExperimental code\n=================\n\nBiopython 1.61 introduced a new warning, ``Bio.BiopythonExperimentalWarning``,\nwhich is used to mark any experimental code included in the otherwise\nstable Biopython releases. Such 'beta' level code is ready for wider\ntesting, but still likely to change, and should only be tried by early\nadopters in order to give feedback via the biopython-dev mailing list.\n\nWe'd expect such experimental code to reach stable status within one or two\nreleases, at which point our normal policies about trying to preserve\nbackwards compatibility would apply.\n\n\nBugs\n====\n\nWhile we try to ship a robust package, bugs inevitably pop up.  If you are\nhaving problems that might be caused by a bug in Biopython, it is possible\nthat it has already been identified. Update to the latest release if you are\nnot using it already, and retry. If the problem persists, please search our\nbug database and our mailing lists to see if it has already been reported\n(and hopefully fixed), and if not please do report the bug. We can't fix\nproblems we don't know about ;)\n\n* Old issue tracker: https://redmine.open-bio.org/projects/biopython\n* Current issue tracker: https://github.com/biopython/biopython/issues\n\nIf you suspect the problem lies within a parser, it is likely that the data\nformat has changed and broken the parsing code.  (The text BLAST and GenBank\nformats seem to be particularly fragile.)  Thus, the parsing code in\nBiopython is sometimes updated faster than we can build Biopython releases.\nYou can get the most recent parser by pulling the relevant files (e.g. the\nones in ``Bio.SeqIO`` or ``Bio.Blast``) from our git repository. However, be\ncareful when doing this, because the code in github is not as well-tested\nas released code, and may contain new dependencies.\n\nFinally, you can send a bug report to the bug database or the mailing list at\nbiopython@biopython.org (subscription required).  In the bug report, please\nlet us know:\n\n1. Which operating system and hardware (32 bit or 64 bit) you are using\n2. Python version\n3. Biopython version (or git commit/date)\n4. Traceback that occurs (the full error message)\n\nAnd also ideally:\n\n5. Example code that breaks\n6. A data file that causes the problem\n\n\nContributing, Bug Reports\n=========================\n\nBiopython is run by volunteers from all over the world, with many types of\nbackgrounds. We are always looking for people interested in helping with code\ndevelopment, web-site management, documentation writing, technical\nadministration, and whatever else comes up.\n\nIf you wish to contribute, please first read `CONTRIBUTING.rst\n<https://github.com/biopython/biopython/blob/master/CONTRIBUTING.rst>`_ here,\nvisit our web site http://biopython.org and join our mailing list:\nhttp://biopython.org/wiki/Mailing_lists\n\n\nDistribution Structure\n======================\n\n- ``README.rst``  -- This file.\n- ``NEWS.rst``    -- Release notes and news.\n- ``LICENSE.rst`` -- What you can do with the code.\n- ``CONTRIB.rst`` -- An (incomplete) list of people who helped Biopython in\n  one way or another.\n- ``CONTRIBUTING.rst`` -- An overview about how to contribute to Biopython.\n- ``DEPRECATED.rst`` -- Contains information about modules in Biopython that\n  were removed or no longer recommended for use, and how to update code that\n  uses those modules.\n- ``MANIFEST.in`` -- Configures which files to include in releases.\n- ``setup.py``    -- Installation file.\n- ``Bio/``        -- The main code base code.\n- ``BioSQL/``     -- Code for using Biopython with BioSQL databases.\n- ``Doc/``        -- Documentation.\n- ``Scripts/``    -- Miscellaneous, possibly useful, standalone scripts.\n- ``Tests/``      -- Regression testing code including sample data files.",
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