Installation
============

You can install shogen by running::

	$ pip install shogen


Usage
=====

Typical usage is::
	
	$ shogen.py [options] genomefile metabolismfile catalysationfile queries
	
	Options:
	  -h, --help   show this help message and exit
	  -k K, --k=K  Number of ranked  shortest genome segments (Default to 5)
	  -l L, --l=L  maximum length of a genome segment (Default to 200)

 
Samples
=======

Sample files for finding functional gene units in e. coli are available here::
      genome.txt_ metabolism.sbml_ catalyze.txt_ queries.txt_

.. _genome.txt: http://bioasp.github.io/downloads/samples/ecoli_K12data/genome.txt
.. _metabolism.txt: http://bioasp.github.io/downloads/samples/ecoli_K12data/metabolism.txt
.. _catalyze.txt: http://bioasp.github.io/downloads/samples/ecoli_K12data/catalyze.txt
.. _queries.txt: http://bioasp.github.io/downloads/samples/ecoli_K12data/queries.txt
