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开源软件名称:biopython/biopython开源软件地址:https://github.com/biopython/biopython开源编程语言:Python 87.5%开源软件介绍:Biopython README fileThe Biopython Project is an international association of developers of freely available Python tools for computational molecular biology. Our user-centric documentation is hosted on https://biopython.org including our API Documentation and the main Biopython Tutorial and Cookbook (PDF). 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 The NEWS file summarises the changes in each release of Biopython. The Biopython package is open source software made available under generous terms. Please see the LICENSE 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 impatientPython 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, Mac OS X 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 RequirementsWe currently recommend using Python 3.9 from http://www.python.org Biopython is currently supported and tested on the following Python implementations:
Optional DependenciesBiopython 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:
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 SourceWe 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:
Then either download and decompress our source code, or fetch it using git. Now change directory to the Biopython source code folder and run: python setup.py build python setup.py test sudo python setup.py install Substitute To exclude tests that require an internet connection (and which may take a
long time), use the python setup.py test --offline If you need to do additional configuration, e.g. changing the install
directory prefix, please type TestingBiopython 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: python setup.py build 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 There is more testing information in the Biopython Tutorial & Cookbook. Experimental codeBiopython 1.61 introduced a new warning, 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. BugsWhile 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 In any bug report, please let us know:
And also ideally:
Contributing, Bug ReportsBiopython 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 here, visit our web site http://biopython.org and join our mailing list: http://biopython.org/wiki/Mailing_lists Distribution Structure
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