skip to navigation
skip to content

shogen 1.4.3

Finding shortest genome segments that regulate metabolic pathways.


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``.


Typical usage is::

$ [options] genomefile metabolismfile catalysationfile queries

-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)


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

.. _genome.txt:
.. _metabolism.txt:
.. _catalyze.txt:
.. _queries.txt:  
File Type Py Version Uploaded on Size
shogen-1.4.3.tar.gz (md5) Source 2014-11-10 8KB
  • Downloads (All Versions):
  • 2 downloads in the last day
  • 102 downloads in the last week
  • 417 downloads in the last month