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Biopython README file
=====================
The Biopython Project is an international association of developers of freely
available Python tools for computational molecular biology.
This README file is intended primarily for people interested in working
with the Biopython source code, either one of the releases from the
http://biopython.org website, or from our repository on GitHub
https://github.com/biopython/biopython
Our user-centric documentation, `The Biopython Tutorial and Cookbook, and API
documentation <https://biopython.org/docs/latest/>`_, is generated from our
repository using Sphinx.
The `NEWS <https://github.com/biopython/biopython/blob/master/NEWS.rst>`_
file summarises the changes in each release of Biopython, alongside the
`DEPRECATED
<https://github.com/biopython/biopython/blob/master/DEPRECATED.rst>`_
file which notes API breakages.
The Biopython package is open source software made available under generous
terms. Please see the `LICENSE
<https://github.com/biopython/biopython/blob/master/LICENSE.rst>`_ file for
further details.
If you use Biopython in work contributing to a scientific publication, we ask
that you cite our application note (below) or one of the module specific
publications (listed on our website):
Cock, P.J.A. et al. Biopython: freely available Python tools for computational
molecular biology and bioinformatics. Bioinformatics 2009 Jun 1; 25(11) 1422-3
https://doi.org/10.1093/bioinformatics/btp163 pmid:19304878
For the impatient
=================
Python includes the package management system "pip" which should allow you to
install Biopython (and its dependency NumPy if needed), upgrade or uninstall
with just one terminal command::
pip install biopython
pip install --upgrade biopython
pip uninstall biopython
Since Biopython 1.70 we have provided pre-compiled binary wheel packages on
PyPI for Linux, macOS and Windows. This means pip install should be quick,
and not require a compiler.
As a developer or potential contributor, you may wish to download, build and
install Biopython yourself. This is described below.
Python Requirements
===================
We currently recommend using Python 3.11 from http://www.python.org
Biopython is currently supported and tested on the following Python
implementations:
- Python 3.9, 3.10, 3.11 and 3.12 -- see http://www.python.org
- PyPy3.9 v7.3.13 -- or later, see http://www.pypy.org
Optional Dependencies
=====================
Biopython requires NumPy (see http://www.numpy.org) which will be installed
automatically if you install Biopython with pip (see below for compiling
Biopython yourself).
Depending on which parts of Biopython you plan to use, there are a number of
other optional Python dependencies, which can be installed later if needed:
- ReportLab, see http://www.reportlab.com/opensource/ (optional)
This package is only used in ``Bio.Graphics``, so if you do not need this
functionality, you will not need to install this package.
- matplotlib, see http://matplotlib.org/ (optional)
``Bio.Phylo`` uses this package to plot phylogenetic trees.
- networkx, see https://networkx.github.io/ (optional) and
pygraphviz or pydot, see https://pygraphviz.github.io/ and
http://code.google.com/p/pydot/ (optional)
These packages are used for certain niche functions in ``Bio.Phylo``.
- rdflib, see https://github.com/RDFLib/rdflib (optional)
This package is used in the CDAO parser under ``Bio.Phylo``.
- psycopg2, see http://initd.org/psycopg/ (optional) or
PyGreSQL (pgdb), see http://www.pygresql.org/ (optional)
These packages are used by ``BioSQL`` to access a PostgreSQL database.
- MySQL Connector/Python, see http://dev.mysql.com/downloads/connector/python/
This package is used by ``BioSQL`` to access a MySQL database, and is
supported on PyPy too.
- mysqlclient, see https://github.com/PyMySQL/mysqlclient-python (optional)
This is a fork of the older MySQLdb and is used by ``BioSQL`` to access a
MySQL database. It is supported by PyPy.
In addition there are a number of useful third party tools you may wish to
install such as standalone NCBI BLAST, EMBOSS or ClustalW.
Installation From Source
========================
We recommend using the pre-compiled binary wheels available on PyPI using::
pip install biopython
However, if you need to compile Biopython yourself, the following are required
at compile time:
- Python including development header files like ``python.h``, which on Linux
are often not installed by default (trying looking for and installing a
package named ``python-dev`` or ``python-devel`` as well as the ``python``
package).
- Appropriate C compiler for your version of Python, for example GCC on Linux,
MSVC on Windows. For Mac OS X, or as it is now branded, macOS, use Apple's
command line tools, which can be installed with the terminal command::
xcode-select --install
This will offer to install Apple's XCode development suite - you can, but it
is not needed and takes a lot of disk space.
Then either download and decompress our source code, or fetch it using git.
Now change directory to the Biopython source code folder and run::
pip install -e .
python setup.py test
sudo python setup.py install
Substitute ``python`` with your specific version if required, for example
``python3``, or ``pypy3``.
To exclude tests that require an internet connection (and which may take a
long time), use the ``--offline`` option::
python setup.py test --offline
If you need to do additional configuration, e.g. changing the install
directory prefix, please type ``python setup.py``.
Testing
=======
Biopython includes a suite of regression tests to check if everything is
running correctly. To run the tests, go to the biopython source code
directory and type::
pip install -e .
python setup.py test
If you want to skip the online tests (which is recommended when doing repeated
testing), use::
python setup.py test --offline
Do not panic if you see messages warning of skipped tests::
test_DocSQL ... skipping. Install MySQLdb if you want to use Bio.DocSQL.
This most likely means that a package is not installed. You can
ignore this if it occurs in the tests for a module that you were not
planning on using. If you did want to use that module, please install
the required dependency and re-run the tests.
Some of the tests may fail due to network issues, this is often down to
chance or a service outage. If the problem does not go away on
re-running the tests, you can use the ``--offline`` option.
There is more testing information in the Biopython Tutorial & Cookbook.
Experimental code
=================
Biopython 1.61 introduced a new warning, ``Bio.BiopythonExperimentalWarning``,
which is used to mark any experimental code included in the otherwise
stable Biopython releases. Such 'beta' level code is ready for wider
testing, but still likely to change, and should only be tried by early
adopters in order to give feedback via the biopython-dev mailing list.
We'd expect such experimental code to reach stable status within one or two
releases, at which point our normal policies about trying to preserve
backwards compatibility would apply.
Bugs
====
While we try to ship a robust package, bugs inevitably pop up. If you are
having problems that might be caused by a bug in Biopython, it is possible
that it has already been identified. Update to the latest release if you are
not using it already, and retry. If the problem persists, please search our
bug database and our mailing lists to see if it has already been reported
(and hopefully fixed), and if not please do report the bug. We can't fix
problems we don't know about ;)
Issue tracker: https://github.com/biopython/biopython/issues
If you suspect the problem lies within a parser, it is likely that the data
format has changed and broken the parsing code. (The text BLAST and GenBank
formats seem to be particularly fragile.) Thus, the parsing code in
Biopython is sometimes updated faster than we can build Biopython releases.
You can get the most recent parser by pulling the relevant files (e.g. the
ones in ``Bio.SeqIO`` or ``Bio.Blast``) from our git repository. However, be
careful when doing this, because the code in github is not as well-tested
as released code, and may contain new dependencies.
In any bug report, please let us know:
1. Which operating system and hardware (32 bit or 64 bit) you are using
2. Python version
3. Biopython version (or git commit/date)
4. Traceback that occurs (the full error message)
And also ideally:
5. Example code that breaks
6. A data file that causes the problem
Contributing, Bug Reports
=========================
Biopython is run by volunteers from all over the world, with many types of
backgrounds. We are always looking for people interested in helping with code
development, web-site management, documentation writing, technical
administration, and whatever else comes up.
If you wish to contribute, please first read `CONTRIBUTING.rst
<https://github.com/biopython/biopython/blob/master/CONTRIBUTING.rst>`_ here,
visit our web site http://biopython.org and join our mailing list:
http://biopython.org/wiki/Mailing_lists
Distribution Structure
======================
- ``README.rst`` -- This file.
- ``NEWS.rst`` -- Release notes and news.
- ``LICENSE.rst`` -- What you can do with the code.
- ``CONTRIB.rst`` -- An (incomplete) list of people who helped Biopython in
one way or another.
- ``CONTRIBUTING.rst`` -- An overview about how to contribute to Biopython.
- ``DEPRECATED.rst`` -- Contains information about modules in Biopython that
were removed or no longer recommended for use, and how to update code that
uses those modules.
- ``MANIFEST.in`` -- Configures which files to include in releases.
- ``setup.py`` -- Installation file.
- ``Bio/`` -- The main code base code.
- ``BioSQL/`` -- Code for using Biopython with BioSQL databases.
- ``Doc/`` -- Documentation.
- ``Scripts/`` -- Miscellaneous, possibly useful, standalone scripts.
- ``Tests/`` -- Regression testing code including sample data files.
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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 3.11 from http://www.python.org\n\nBiopython is currently supported and tested on the following Python\nimplementations:\n\n- Python 3.9, 3.10, 3.11 and 3.12 -- see http://www.python.org\n\n- PyPy3.9 v7.3.13 -- or later, see http://www.pypy.org\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 https://networkx.github.io/ (optional) and\n pygraphviz or pydot, see https://pygraphviz.github.io/ 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 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 PyPy.\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 required\nat compile time:\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 package).\n\n- Appropriate C compiler for your version of Python, for example GCC on Linux,\n MSVC on Windows. 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To run the tests, go to the biopython source code\ndirectory and type::\n\n pip install -e .\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\nIssue 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\nIn any bug report, please let us know:\n\n1. 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