shogen

Finding shortest genome segments that regulate metabolic pathways

Project description

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

Project details

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1.4.3

Nov 10, 2014

1.4.2

May 21, 2014

1.4.1

Mar 6, 2014

This version

1.4

Mar 4, 2014

1.3

Jan 21, 2014

1.2

Aug 23, 2013

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