Metadata-Version: 1.1
Name: ypkpathway
Version: 0.8.4
Summary: Assemble metabolic pathways from the command line using the ypkpathway protocol
Home-page: http://pypi.python.org/pypi/ypkpathway/
Author: Björn Johansson
Author-email: bjorn_johansson@bio.uminho.pt
License: LICENSE.txt
Description: ==========
        ypkpathway
        ==========
        
        .. image:: https://travis-ci.org/BjornFJohansson/ypkpathway.svg
            :target: https://travis-ci.org/BjornFJohansson/ypkpathway
        
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            :target: https://ci.appveyor.com/project/BjornFJohansson/ypkpathway
        
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            :alt: Downloads
        
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            :alt: Latest Version
        
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        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 in FASTA or Genbank format 
        to be assembled. The ypkpathway command above creates a folder with a series of
        IPython notebooks describing the assembly process simulated with pydna. Help is available by the -h option:
        
            bjorn@bjorn-UL30A:/$ ypkpathway -h
            Usage: ypkpathway <path> [<dir>]
                   ypkpathway -h|--help
                   ypkpathway -v|--version
                   ypkpathway -t|--test
        
            Arguments:
                <path>  path to data file containing sequences to be assembled
        
                <dir>   Directory to put generated sequence files,defaults to
                        <ypk_assembly> in the current working directory.
        
            Options:
                -h, --help      Show this screen.
                -v, --version   Show version.
                -t, --test      Run tests.
        
        
        The results folder will include:
        
        * The sequence of the final pathway and all intermediate vectors in Genbank format
        * IPython notebooks file describing the final assembly and intermediate assemblies.
        * All PCR primers needed for the amplification of pathway components.
        * Expected diagnostic PCR product fragment lengths indicating correct and incorrect clonings.
        
        
        NEWS
        ====
        
        =======   ========== =============================================================
        version   date       comment
        =======   ========== =============================================================
        0.8.4     2015-05-30 An IPython.display.FileLink object is now returned from the 
                             ypkpathway function.
        
        0.8.3     2015-05-29 windows fix for opening final pathway notebook.
        
        0.8.2     2015-05-28 pydna dependency 0.9.2, fix a unicode env variable.
        
        0.8.1     2015-05-26 pydna dependency 0.9.1
        
        0.8.0     2015-05-26 Complete change in functionality. IPython notebook files are
                             generated and executed instead of rst and html files.
        
        0.6.0     2015-04-17 Added nosetests
        
        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>=0.9.1 <https://pypi.python.org/pypi/pydna/>`_.
        
        - `ipython>=3.1.0 <https://pypi.python.org/pypi/ipython/>`_.
        
        - `docopt>=0.6.2 <https://pypi.python.org/pypi/docopt/>`_.
        
        - `notedown>=1.4.4 <https://pypi.python.org/pypi/notedown/>`_.
        
        
        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 installed. 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.
        
        Testing
        -------
        
        Nose is needed to run the test suit.
        
            sudo pip install nose <enter>
        
        Then from the source directory do:
        
            python run_tests.py
        
        Distribution Structure
        ======================
        
        README.rst          -- 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>
        
        ypkpathway/         -- The actual code.
        
        docs/               -- Documentation.
        
        tests/              -- Testing code and data.
        
Keywords: bioinformatics
Platform: UNKNOWN
Classifier: Development Status :: 4 - Beta
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
