genonets 1.0.0b3

Framework for creating and analyzing genotype networks from data.

This is the Python package used by the Genonets Server for creating and analyzing genotype networks from raw data.

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Installation

Linux and Mac OS

Using pip,

pip install genonets

In case you get a ‘permission’ related error, try the following:

sudo pip install 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

Windows

Instructions for Windows are basically the same, except in certain cases installation of dependencies fails. If that happens, follow these steps:

1. Download the ‘whl’ files for numpy and igraph from http://www.lfd.uci.edu/~gohlke/pythonlibs/. E.g.,

   1. numpy-1.10.2+mkl-cp27-none-win32.whl

   2. python_igraph-0.7.1.post6-cp27-none-win32.whl

3. pip install python_igraph-0.7.1.post6-cp27-none-win32.whl

4. pip install numpy-1.10.2+mkl-cp27-none-win32.whl

5. And finally, pip install genonets

Using Genonets as a command line tool

The best way to get started is to work through ‘genonets_exmpl_simple.py’ available in the ‘genonets/sample’ directory. The following command can be used to view the list of command line arguments:

‘python genonets_exmpl_simple.py -h’

This directory also includes other sample files, each highlighting different features.

The details of the analyses used and the attributes computed can be found on the Learn Genonets page.