Metadata-Version: 1.0
Name: python-dna
Version: 0.0.7
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/python-dna/
Author: Björn Johansson
Author-email: bjorn_johansson@bio.uminho.pt
License: LICENSE.txt
Description: ==========
        Python-dna
        ==========
        
        Python dna 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 class "drecord", which is a subclass of
        the `Biopython <http://biopython.org/wiki/Main_Page>`_. SeqRecord class.
        
        Python-DNA 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.
        
        Python-dna was designed to semantically imitate how sub cloning experiments are
        typically documented in Scientific literature. Python-dna code describing a
        sub cloning is reasonably compact and meant to be easily readable.
        
        One use case for Python-dna is to create a sort of executable documentation
        describing a subcloning experiment. The Python-dna code unambiguously describe
        a sub cloning experiment, and can be executed to yield the sequence of the
        of the resulting DNA molecule.
        
        Typical usage at the command line could look like this::
        
            #!/usr/bin/env python
        
            >>> 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!
            >>>
        
        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 Python-dna 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/python-dna/#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>
        
        
        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/              -- Regression testing code
        
        
        
        
        
        
        
        
        
Platform: UNKNOWN
