Framework for creating and analyzing genotype networks from data.
Project description
This is the Python package used by the Genonets Server for creating and analyzing genotype networks from raw data. The details of the analyses used and the attributes computed can be found on the Learn Genonets page.
Installation
Linux and Mac OS
Using pip,
pip install --pre genonets
In case you get a ‘permission’ related error, try the following:
sudo pip install --pre genonets
You can also install Genonets directly from the source package.
python setup.py install
Again, in case you run into permission related errors,
sudo python setup.py install
When trying to install genonets on a machine with Ubuntu 14.04 LTS that does not already have the required version of python-igraph installed, pip sometimes fails to install the C core of igraph. If that happens, follow these steps:
sudo apt-get install build-essential
sudo apt-get python-dev
sudo apt-get install libxml2-dev
sudo apt-get install libz-dev
sudo pip uninstall genonets
Finally, sudo pip install --pre genonets
Windows
Instructions for Windows are basically the same, except in certain cases installation of dependencies fails. If that happens, follow these steps:
- Download the ‘whl’ files for numpy and python-igraph from http://www.lfd.uci.edu/~gohlke/pythonlibs/. E.g.,
numpy-1.10.2+mkl-cp27-none-win32.whl
python_igraph-0.7.1.post6-cp27-none-win32.whl
pip install python_igraph-0.7.1.post6-cp27-none-win32.whl
pip install numpy-1.10.2+mkl-cp27-none-win32.whl
And finally, pip install --pre genonets
Genonets quick start
The best way to get started is to work through genonets_exmpl_simple.py available in the genonets/genonets/sample directory. In case you cannot locate the directory in which genonets is installed, you can download the sample code from the genonets PyPI page.
To get started, first copy the sample folder in a directory with write privileges. Then, try the following command:
python genonets_exmpl_simple.py DNA true data/genonets_sample_input.txt 0.35 results_simple
This command does the following:
Parses the sample input file located in the data directory
Creates genotype networks for all available genotype sets
Performs all available analyses on the genotype sets
- Writes the following in the in the results_simple directory:
A file with genotype network level attributes for all genotype sets
For each genotype network, a file with genotype level attributes
GML files for genotype networks
The following command can be used to view a description of command line arguments:
python genonets_exmpl_simple.py -h
The genonets/genonets/sample directory also includes other sample files, each highlighting different features.
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