Metadata-Version: 1.1
Name: ypkpathway
Version: 0.5.0
Summary: Assemble metabolic pathways from the command line
Home-page: http://pypi.python.org/pypi/py-genome/
Author: Björn Johansson
Author-email: bjorn_johansson@bio.uminho.pt
License: LICENSE.txt
Description: ==========
        ypkpathway
        ==========
        
        Ypkpatwhay provides a command line application for planning DNA assembly projects 
        using the Yeast Pathway Kit protocol. 
        
        Typical usage at the command line could look like this::
        
            bjorn@bjorn-UL30A:/$ ypkpathway four_gene_xylose_pathway.txt
            
        Where four_gene_xylose_pathway1.txt is a text file containing DNA sequences to be assembled
        in FASTA or Genbank format. See documentation for file format.
        
        The ypkpathway creates a subdirectory called generates a sub directory called "ypk_assembly".
        This subdirectory will contain a file summary of the DNA assembly project called report.html 
        which can be opened in a web browser. 
        
        The report will include:
        
        * The sequence of the final pathway
        * Sequences of all generated intermediate vectors
        * All PCR primers needed for the amplification of pathway components
        * Diagnostic PCR product fragment lengths indicating correct and incorrect clonings
        
        
        ypkpathway depends on the `pydna <https://pypi.python.org/pypi/pydna/>`_ package.
        
        
        
        NEWS
        ====
        
        =======   ========== =============================================================
        version   date       comment
        =======   ========== =============================================================
        
        0.5.0	  2014-12-09 Changed to work with new caching version of pydna. Fixed 
        				     unicode errors.
        
        0.0.9     2014-06-14 bugfix
                             changed errors in automatically generated pydna source files
                             
        0.0.8     2014-05-14 first release
        
        =======   ========== =============================================================
        
        System Requirements
        ===================
        
        - `Python 2.7 <http://www.python.org>`_.
        
        - `pydna>=0.7.2 <https://pypi.python.org/pypi/pydna/>`_.
        
        - `docutils>=0.11 <https://pypi.python.org/pypi/docutils/>`_.
        
        - `docopt>=0.6.1 <https://pypi.python.org/pypi/docopt/>`_.
        
        
        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 tested with python 3.
        
        Installation
        ============
        
        The best way of installing ypkpathway is with `pip <https://pypi.python.org/pypi/pip/>`_::
        
            sudo pip install ypkpathway <enter>
            
        Pip will take care of the installation of any missing dependencies.
        
        Source
        ------
        
        Make sure all dependencies are intalled. 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.
        
        Distribution Structure
        ======================
        
        README.txt          -- This file.
        
        LICENSE.txt         -- What you can do with the code.
        
        MANIFEST.in         -- Tells distutils what files to distribute
        
        setup.py            -- Installation file.
        
        run_tests.py        -- run tests by "python run_tests.py"<enter> (Currently empty)
        
        ypkpathway/         -- The actual code.
        
        docs/               -- Documentation.
        
        tests/              -- Testing code and data.
        
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
