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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

Project details


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This version
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1.4.3

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1.4.2

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1.4

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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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