Metadata-Version: 1.1
Name: pydna
Version: 0.1.5
Summary: Contains classes and code for representing double
                     stranded DNA and functions for simulating homologous
                     recombination between DNA molecules.
Home-page: http://pypi.python.org/pypi/pydna/
Author: Björn Johansson
Author-email: bjorn_johansson@bio.uminho.pt
License: LICENSE.txt
Description: =====
        pydna
        =====
        
        Pydna provide classes and functions for molecular biology using python.
        Notably, PCR, cut and paste cloning and homologous recombination between linear
        DNA fragments are supported. Most functionality is implemented as methods for
        the double stranded DNA sequence record classes Dseq and Dseqrecord, which
        are subclasses of the `Biopython <http://biopython.org/wiki/Main_Page>`_
        `Seq <http://biopython.org/wiki/Seq>`_
        and
        `SeqRecord <http://biopython.org/wiki/SeqRecord>`_ classes.
        
        Pydna might be useful to automate the simulation of
        `sub cloning <http://en.wikipedia.org/wiki/Subcloning>`_ experiments using
        python. This could be helpful to generate examples for teaching purposes. Read
        the `documentation <https://pydna.readthedocs.org/en/latest/>`_ or the
        `cookbook <https://pydna.googlecode.com/files/cookbook.zip>`_ with example files
        for further information.
        
        Pydna was designed to semantically imitate how sub cloning experiments are
        typically documented in Scientific literature. Pydna code describing a
        sub cloning is reasonably compact and meant to be easily readable.
        
        One use case for pydna is to create executable documentation
        describing a subcloning experiment. The pydna code unambiguously describe
        a sub cloning experiment, and can be executed to yield the sequence of the
        of the resulting DNA molecule.
        
        An `on-line <http://pydna-shell.appspot.com/>`_ shell running Python with
        pydna is avaiable for experimentation.
        
        Please post a message in the `google group <https://groups.google.com/d/forum/pydna>`_
        for pydna if you have problems, questions or comments.
        
        Feedback is very welcome!
        
        Typical usage at the command line could look like this::
        
            >>> import pydna
            >>> seq = pydna.Dseq("GGATCCAAA","TTTGGATCC",ovhg=0)
            >>> seq
            Dseq(-9)
            GGATCCAAA
            CCTAGGTTT
            >>> from Bio.Restriction import BamHI
            >>> a,b = seq.cut(BamHI)
            >>> a
            Dseq(-5)
            G
            CCTAG
            >>> b
            Dseq(-8)
            GATCCAAA
                GTTT
            >>> a+b
            Dseq(-9)
            GGATCCAAA
            CCTAGGTTT
            >>> b+a
            Dseq(-13)
            GATCCAAAG
                GTTTCCTAG
            >>> b+a+b
            Dseq(-17)
            GATCCAAAGGATCCAAA
                GTTTCCTAGGTTT
            >>> b+a+a
            Traceback (most recent call last):
              File "<stdin>", line 1, in <module>
              File "/usr/local/lib/python2.7/dist-packages/pydna/dsdna.py", line 217, in __add__
                raise TypeError("sticky ends not compatible!")
            TypeError: sticky ends not compatible!
            >>>
        
        NEWS
        ====
        
        =======   ========== =============================================================
        version   date       comment
        =======   ========== =============================================================
        0.1.5     2013-04-18 Changed the setup.py script to permit installation
                             of the source installer without access to a c compiler.
        
        0.1.4     2013-04-10 Cleaned up some docstrings
                             Renamed Drecord -> Dseqrecord to be more consistent with
                             Dseq and Biopython Seq/SeqRecord.
        
                             Changed name of keyword argument for read and parse.
                             ds=True returns Dseqrecord(s) while ds=False returns
                             SeqRecords.
        
        0.1.3     2013-04-09 pydna created from Python-dna.
        
        =======   ========== =============================================================
        
        System Requirements
        ===================
        
        - `Python 2.7 <http://www.python.org>`_.
        
        - `NumPy >= 1.6.1 <http://pypi.python.org/pypi/numpy>`_.
        
        - `Biopython >= 1.60 <http://pypi.python.org/pypi/biopython>`_.
        
        - `networkx >= 1.7 <http://pypi.python.org/pypi/networkx>`_.
        
        - `distribute >= 0.6.34 <http://pypi.python.org/pypi/distribute>`_.
        
        Python 2.x
        ----------
        
        Versions other than 2.7 has not been tried with this software.
        Version 2.7.3 was used to build the distribution.
        
        Python 3.x
        ----------
        
        This code has not been tried with python 3.
        
        Installation
        ============
        
        Source
        ------
        
        You need to install the dependencies listed above.
        If you are using Windows, you need to have a C compiler installed.
        The free MS visual studio 2008 express can be used.
        
        Open the pydna source code directory (containing the setup.py file) in
        terminal and type:
        
            sudo python setup.py install <enter>
        
        If you need to do additional configuration, e.g. changing the base
        directory, please type `python setup.py`, or see the documentation for
        Setuptools.
        
        
        Binary distribution
        -------------------
        
        A `Binary installer <http://pypi.python.org/pypi/pydna/#downloads>`_ for 32 bit editions of MS Windows XP and 7 are provided.
        
        The installer has been tested on succesfully on both.
        
        The dependencies have to be installed from source or using binary installers
        for 32 bit windows.
        
        This is a list of locations of binary installers:
        
        - Python          <http://www.python.org/download/>
        - NumPy           <http://sourceforge.net/projects/numpy/files/NumPy/>
        - Biopython       <http://biopython.org/wiki/Download>
        - networkx        <http://www.lfd.uci.edu/~gohlke/pythonlibs/#networkx>
        
        
        Source Code Repository
        ----------------------
        
        pydna is hosted by google code:
        
        http://code.google.com/p/pydna/
        
        
        Distribution Structure
        ======================
        
        README.txt          -- This file.
        
        NEWS.txt            -- Release notes and news
        
        LICENSE.txt         -- What you can do with the code.
        
        MANIFEST.in         -- Tells distutils what files to distribute
        
        setup.py            -- Installation file.
        
        setup_build.py      -- Building from Cython source (not needed for install)
        
        distribute_setup.py -- Bootstrap distribute installation for version 0.6.34 which will pretend to be setuptools 0.6c11
        
        run_tests.py        -- run tests by "python run_tests.py"<enter>
        
        pydna/              -- The actual code.
        
        docs/                -- Documentation.
        
        scripts/            -- Miscellaneous perhaps useful scripts
        
        tests/              -- Testing code
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 2.7
Classifier: Topic :: Education
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
