ypkpathway 0.0.9

Assemble metabolic pathways from the command line

==========
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
====

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version date comment
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0.0.9 2014-06-14 bugfix
changed errors in automatically generated pydna source files

0.0.8 2014-05-14 first release

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System Requirements
===================

- `Python 2.7 <http://www.python.org>`_.

- `pydna>=0.6.1 <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.