Metadata-Version: 1.1
Name: ypkpathway
Version: 1.0.0a13
Summary: Simulation and documentation of metabolic pathway assemblies using the Yeast Pathway Kit.
Home-page: http://pypi.python.org/pypi/ypkpathway/
Author: Björn Johansson
Author-email: bjorn_johansson@bio.uminho.pt
License: LICENSE.txt
Description: 
        |icon| ypkpathway
        =================
        
        Ypkpathway is a simulator and documentation generator for *in-vivo*
        pathway assembly using the Yeast Pathway Kit protocol. It takes as
        argument a series of sequences in a text file and produces a self
        contained folder containing assembled sequences of intermediary vectors,
        final assembly and PCR primers. Other useful information such as PCR
        conditions and PCR product sizes for construction and confirmation are
        also included. The documantation of the assembly is given in the
        narrative IPython notebook format which can be executed independently of
        ypkpathway.
        
        The assembly process is simulated using
        `pydna <https://github.com/BjornFJohansson/pydna>`__ in `IPython
        notebooks <http://ipython.org/notebook.html>`__ which are automatically
        generated and executed.
        
        See an example of a four gene assembly
        `here <http://nbviewer.ipython.org/github/BjornFJohansson/ypkpathway/blob/master/docs/pth6/pw.ipynb>`__.
        The notebooks in the example are located in the docs folder in this
        repository and visualized through
        `nbviewer <http://nbviewer.ipython.org/>`__. The example above was made
        with the
        `pth6 <http://nbviewer.ipython.org/github/BjornFJohansson/ypkpathway/blob/master/tests/pth6.txt>`__
        indata.
        
        Version 1.0.0 runs on Python 3.5 or 3.6 and depends on pyqt5 and pydna
        2.0.0 or later. The pydna code generated by ypkpathway 1.0.0 also need
        pydna 2.0.0 or later to run.
        
        There are five more example indata files that are a part of the
        automatic test suit:
        `pth1 <http://nbviewer.ipython.org/github/BjornFJohansson/ypkpathway/blob/master/tests/pth1.txt>`__
        `pth2 <http://nbviewer.ipython.org/github/BjornFJohansson/ypkpathway/blob/master/tests/pth2.txt>`__
        `pth3 <http://nbviewer.ipython.org/github/BjornFJohansson/ypkpathway/blob/master/tests/pth3.txt>`__
        `pth4 <http://nbviewer.ipython.org/github/BjornFJohansson/ypkpathway/blob/master/tests/pth4.txt>`__
        `pth5 <http://nbviewer.ipython.org/github/BjornFJohansson/ypkpathway/blob/master/tests/pth5.txt>`__
        `pth7 <http://nbviewer.ipython.org/github/BjornFJohansson/ypkpathway/blob/master/tests/pth7.txt>`__
        
        |screenshot|
        
        |pypi| Python wheel and source distributions on Pypi.
        
        |travis| Conda packages for MacOSX built on TravisCI.
        
        |appveyor| Conda packages built on Appveyor-CI.
        
        |CircleCI| Conda packages for Linux built on CircleCI.
        
        |anaconda| Anaconda download count.
        
        |GitHub tag| Github repository.
        
        The ypkpatwhay package provides a graphical point and click interface
        and a command line application for planning DNA assembly projects using
        the Yeast Pathway Kit protocol.
        
        Please refer to the
        `manual <https://github.com/BjornFJohansson/ypkpathway/blob/master/docs/manual.pdf>`__
        for details on how to use the software.
        
        Installation
        ------------
        
        The best way of installing ypkpathway is by first installing the free
        `Anaconda Python
        distribution <https://store.continuum.io/cshop/anaconda/>`__ which comes
        with many packages and dependencies out of the box. Using the conda
        package manages simply type:
        
        ::
        
            bjorn@bjorn-UL30A:/$ conda install ypkpathway
        
        and the app and all dependencies will be installed. The
        `manual <https://github.com/BjornFJohansson/ypkpathway/blob/master/docs/manual.pdf>`__
        contains a detailed walk through of this installation option.
        
        Alternatively, ypkpathway can be installed using
        `pip <https://pypi.python.org/pypi/pip>`__ which is the `PyPA
        recommended <https://python-packaging-user-guide.readthedocs.org/en/latest/current.html>`__
        tool for installing Python packages.
        
        ::
        
            bjorn@bjorn-UL30A:/$ pip install ypkpathway
        
        Pip may have trouble to install two dependecies
        `biopython <https://pypi.python.org/pypi/biopython>`__ which is a
        dependency of pydna and
        `PyQt4 <https://pypi.python.org/pypi/PyQt4/4.11.4>`__ which have binary
        extensions. These can be separately installed. Binary installers of
        PyQt4 can be found
        `here <http://www.riverbankcomputing.com/software/pyqt/download>`__.
        Instructions for how to install Biopython can be found
        `here <http://biopython.org/wiki/Download>`__.
        
        Ypkpathway can also be installed from source by downloading one of the
        source distributions. Unpack the zip or .tar.gz archive and type:
        
        ::
        
            bjorn@bjorn-UL30A:/$ python setup.py install
        
        Dependencies has to be manually installed in this case. There are also
        .exe installers for ypkpathway that can be installed by double clicking.
        These do not install the dependencies either.
        
        Dependencies
        ------------
        
        The ypkpathway dependencies are pure Python modules except for PyQt.
        Pydna depends on `biopython <https://pypi.python.org/pypi/biopython>`__
        which has to be installed using a binary installer or else a C compiler
        has to be available.
        
        `pydna <https://pypi.python.org/pypi/pydna>`__
        
        `ipython <https://pypi.python.org/pypi/ipython>`__
        
        `notedown <https://pypi.python.org/pypi/notedown>`__
        
        `nbformat <https://pypi.python.org/pypi/nbformat/4.3.0>`__
        
        `PyQt5 <https://pypi.python.org/pypi/PyQt5>`__
        
        `docopt <https://pypi.python.org/pypi/docopt>`__
        
        There are binary Windows installers for IPython, Bioppython, docopt
        `here <http://www.lfd.uci.edu/~gohlke/pythonlibs/>`__
        
        Graphical user interface
        ------------------------
        
        The application is written in PyQt4 and can be started from the command
        line by typing ypkpathway and pressing :
        
        ::
        
            bjorn@bjorn-UL30A:/$ ypkpathway
        
        It can also be started from the Anaconda Launcher if installed using
        conda on the Anaconda Python distribution.
        
        Command line interface
        ----------------------
        
        Typical usage at the command line could look like this:
        
        ::
        
            bjorn@bjorn-UL30A:/$ ypkpathway_cli pth6.txt
        
        Where pth6.txt is a text file containing DNA sequences in FASTA or
        Genbank format to be assembled as described in the
        `manual <https://github.com/BjornFJohansson/ypkpathway/blob/master/docs/manual.pdf>`__.
        
        The ypkpathway\_cli 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.
        
        Results
        -------
        
        The ypkpathway and ypkpathway\_cli both produce the same result, which
        is a results folder containing a selection of files. The folder will
        contain:
        
        -  The sequence of the final pathway and all intermediate vectors in
           `Genbank <http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html>`__
           format
        -  IPython notebooks files 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.
        
        The IPython notebook files in the results folder can be viewed with a
        web browser with oly IPython is installed on the computer. There are
        static versions of the notebook files that can be viewed with only a web
        browser (not eve Python is required).
        
        Development
        -----------
        
        Ypkpathway is open source software and developed on Github |GitHub tag|.
        
        How it works
        ------------
        
        Ypkpathway generates a series of text documents in
        `markdown <http://daringfireball.net/projects/markdown/>`__ format that
        are formatted with the given data. There is one document per vector
        generated in in the assembly process. These documents contain comments
        and links as well as Python code. The python code describe the cloning
        and assembly steps using pydna.
        
        The markdown documents are turned into JSON format using the
        `notedown <https://github.com/aaren/notedown>`__ package.
        
        The notebooks are executed using IPython. All files and raw data are
        saved in a self contained result folder.
        
        .. |icon| image:: https://raw.githubusercontent.com/BjornFJohansson/ypkpathway/master/icon.resized.png
           :target: https://pypi.python.org/pypi/ypkpathway/
        .. |screenshot| image:: https://raw.githubusercontent.com/BjornFJohansson/ypkpathway/master/screenshot.resized.png
           :target: https://github.com/BjornFJohansson/ypkpathway
        .. |pypi| image:: https://img.shields.io/pypi/v/ypkpathway.png
           :target: https://pypi.python.org/pypi/ypkpathway/
        .. |travis| image:: https://travis-ci.org/BjornFJohansson/ypkpathway.svg
           :target: https://travis-ci.org/BjornFJohansson/ypkpathway
        .. |appveyor| image:: https://ci.appveyor.com/api/projects/status/ol5ru8po7fx5cimj?svg=true
           :target: https://ci.appveyor.com/project/BjornFJohansson/ypkpathway
        .. |CircleCI| image:: https://circleci.com/gh/BjornFJohansson/ypkpathway.svg?style=svg
           :target: https://circleci.com/gh/BjornFJohansson/ypkpathway
        .. |anaconda| image:: https://anaconda.org/bjornfjohansson/ypkpathway/badges/downloads.svg
           :target: https://anaconda.org/bjornfjohansson/ypkpathway
        .. |GitHub tag| image:: https://img.shields.io/github/tag/BjornFJohansson/ypkpathway.svg
           :target: https://github.com/BjornFJohansson/ypkpathway
        
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 :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Education
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
