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CoreBio is a python toolkit for writing computational biology applications. For further information on the CoreBio API, please consult the source code or the API docmentation at 'docs/apidocs/index.html'. o data: Standard information used in computational biology. o db: Database access: astral, scop ... o moremath: Various bits of useful math not in the standard python library. o secstruc: Protein secondary structure and associated tools and data. o seq: Alphabetic sequences and associated tools and data. o seq_io: Sequence file reading and writing: array, clustal, fasta, genbank, intelligenetics, msf, nbrf, nexus, phylip, plain, stockholm, tabular. o ssearch_io: Parse the output of BLAST and similar sequence search reports. o transform: Transformations of Seqs (alphabetic sequences). o utils: Extra utilities and core classes not in standard python. ------------ Installation ------------ CoreBio requires python version 2.3, 2.4 or 2.5. The following command will quickly determine if python is available. (Download python : http://www.python.org/download/) > python -V Python 2.4.2 If you have setuptools installed (http://peak.telecommunity.com/DevCenter/), then installation can be accomplished with a single command: > sudo easy_install corebio Or to upgrade: > sudo easy_install -U corebio Alternativly, download the latest distribution from the project home page, http://code.google.com/p/corebio/ > curl http://corebio.googlecode.com/svn/dist/CoreBio-X.X.X.tar.gz >CoreBio.tar.gz > tar -zxf CoreBio.tar.gz > cd CoreBio-X.X.X To install corebio from the main CoreBio directory: > python setup.py --help install # Show installation options > python setup.py install # Install code. > python setup.py install --home ~/local # Install into alternative location --------------------------------------- Development and Subversion Installation --------------------------------------- To modify or extent CoreBio, or to use the latest code, obtain the source directly from the subversion repository. (Subversion clients can be obtained at http://subversion.tigris.org) > svn checkout http://corebio.googlecode.com/svn/trunk/ corebio See the DEVELOPERS.txt file for more information. ----------------------------- Distribution and Modification ----------------------------- This package is distributed under the new BSD Open Source License. Please see the LICENSE.txt file for details on copyright and licensing. |
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