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.
Installation
Linux and Mac OS
Using pip,
pip install genonets-1.0.0-py2-none-any.whl
In case you get a ‘permission’ related error, try the following:
sudo pip install genonets-1.0.0-py2-none-any.whl
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 are basically the same, except in certain case installation of dependencies fails. In case that happens, follow these steps:
- Download the ‘whl’ files for numpy and 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 genonets-1.0.0-py2-none-any.whl
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.
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