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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

Release History

This version
History Node

1.4.3

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1.4.2

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1.4.1

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1.4

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1.3

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1.2

Download Files

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Filename, Size & Hash SHA256 Hash Help File Type Python Version Upload Date
shogen-1.4.3.tar.gz
(8.4 kB) Copy SHA256 Hash SHA256
Source None Nov 10, 2014

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