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
============
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
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