shogen2

Finding shortest genome segments that regulate metabolic pathways

Project description

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

You can install shogen2 by running::

$ pip install shogen2

Usage
=====

Typical usage is::

$ shogen2.py [options] genomefile metabolismfile.sbml 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://www.cs.uni-potsdam.de/~sthiele/bioasp/downloads/samples/ecoli_K12data/genome.txt
.. _metabolism.sbml: http://www.cs.uni-potsdam.de/~sthiele/bioasp/downloads/samples/ecoli_K12data/metabolism.sbml
.. _catalyze.txt: http://www.cs.uni-potsdam.de/~sthiele/bioasp/downloads/samples/ecoli_K12data/catalyze.txt
.. _queries.txt: http://www.cs.uni-potsdam.de/~sthiele/bioasp/downloads/samples/ecoli_K12data/queries.txt

Project details

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1.1.1

Mar 6, 2014

1.1

Mar 4, 2014

This version

1.0

Jan 16, 2014

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