genonets 1.0.4

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. 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 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

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:

1. sudo apt-get install build-essential

2. sudo apt-get python-dev

3. sudo apt-get install libxml2-dev

4. sudo apt-get install libz-dev

5. sudo pip uninstall genonets

6. Finally, sudo pip install genonets

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 python-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

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 source tarball from the genonets PyPI page, and find the sample folder inside the extracted genonets directory.

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:

1. Parses the sample input file located in the data directory

2. Creates genotype networks for all available genotype sets

3. Performs all available analyses on the genotype sets

4. Writes the following in the in the results_simple directory:

   1. A file with genotype network level attributes for all genotype sets

   2. For each genotype network, a file with genotype level attributes

   3. 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.