==========
ypkpathway
==========

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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 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.


NEWS
====

=======   ========== =============================================================
version   date       comment
=======   ========== =============================================================
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 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.
