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shogen 1.4.3

Finding shortest genome segments that regulate metabolic pathways.

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

You can install shogen by running::

$ pip install --user shogen

On Linux the executable script can then be found in ``~/.local/bin``

and on MacOS the script is under ``/Users/YOURUSERNAME/Library/Python/2.7/bin``.

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.txt_ 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  
File Type Py Version Uploaded on Size
shogen-1.4.3.tar.gz (md5) Source 2014-11-10 8KB
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