Finding shortest genome segments that regulate metabolic pathways.
Project description
Installation
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.
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.txt catalyze.txt queries.txt
