Skip to main content

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

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

shogen-1.4.3.tar.gz (8.4 kB view hashes)

Uploaded source

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page