shogen
Finding shortest genome segments that regulate metabolic pathways
Finding shortest genome segments that regulate metabolic pathways
Integrating heterogeneous knowledge is necessary to elucidate the regulations in biological systems. In particular, such an integration is widely used to identify functional units, that are sets of genes that can be triggered by the same external stimuli, as biological stresses, and that are linked to similar responses of the system. Although several models and algorithms shown great success for detecting functional units on well-known biological species, they fail in identifying them when applied to more exotic species, such as extremophiles, that are by nature unrefined. Shortest Genome Segments (SGS) is a new model of functional units with a predictive power that is comparable to existing methods but overcomes this crucial limitation. In contrary to existing methods, SGS are stable in (i) computational time and (ii) ability to predict functional units when one deteriorates the biological knowledge, which simulates cases that occur for exotic species.
You can install shogen by running:
$ pip install --user shogen
On Linux the executable script can then be found in ~/.local/bin
and on Mac OS the script is under /Users/YOURUSERNAME/Library/Python/2.7/bin.
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)
Sample files for finding functional gene units in e. coli are available here: genome.txt metabolism.txt catalyze.txt queries.txt
Q: I don't have pip. How can I install pip without admin rights?
A: You can install pip without admin rights.
Download getpip.py.
$ wget https://raw.github.com/pypa/pip/master/contrib/get-pip.py
Install pip locally.
$ python get-pip.py --user
You can install using your local pip.
Q: I don't have pip. How can I install shogen without pip?
A: You can install shogen without pip if you take care of the dependencies yourself.
Download pyasp-1.3.3.
$ wget https://pypi.python.org/packages/source/p/pyasp/pyasp-1.3.3.tar.gz
Extract and install pyasp.
$ gzip -d pyasp-1.3.3.tar.gz
$ tar -xvf pyasp-1.3.3.tar
$ cd pyasp-1.3.3
$ python setup.py install --user
Download shogen-1.4.3.
$ wget https://pypi.python.org/packages/source/s/shogen/shogen-1.4.3.tar.gz
Extract and install shogen.
$ gzip -d shogen-1.4.3.tar.gz
$ tar -xvf shogen-1.4.3.tar
$ cd shogen-1.4.3
$ python setup.py install --user
The executable script can then be found in ~/.local/bin on Linux and in /Users/YOURUSERNAME/Library/Python/2.7/binon Mac OS.