1. Cheng Soon Ong
  2. chillo

Overview

Copyright 2012, 2013, Cheng Soon Ong, Ilana Lichtenstein, Cristovao Freitas Iglesias Junior NICTA

Install

python setup.py install --prefix=/path/to/lib

Do not forget to add /path/to/lib to $PYTHONPATH. For example: export PYTHONPATH=$HOME/lib/python2.7/site-packages/:$PYTHONPATH

Testing

Typing $ nosetests into the terminal in this directory runs all the tests in the test directory. This requires the package 'nose'

External code

link_clustering.py from Jim Bagrow, Yong-Yeol Ahn

Notes from Cristovao

sudo vi /etc/bash.bashrc and inside bash.bashrc I put -> export PYTHONPATH=$HOME/epistasis/GraphEnrich:$PYTHONPATH with this I can use "from chillo.graph import GWISGraph" for test use: "python test/test_link_cluster.py"

Summary of Scripts written or used by Ilana

There are 4 scripts to deal with 4 possibilities of SnpGraph vs GeneGraph (JSON needs SnpGraph) reading in from 3-column csv file vs multi-column spreadsheet

gwis2graph.py

reads in results as 3 column csv file (snp,snp,score) initialise a SnpGraph outputs JSONs

process_WTCCC_gwis_results.py

reads in results as 3 column csv file (snp,snp,score) initialise a GeneGraph perform multiple steps in network feature analysis, gene set over-representation analysis

gss2graph.py

reads in results as multicolumn spreadsheet with multiple tests initialise a SnpGraph outputs JSONs

process_WTCCC.py

python process_WTCCC.py config_wtccc.py

(Insert name of your configuration file).

reads in results as multicolumn spreadsheet with multiple tests initialise a GeneGraph and save load GeneGraph and perform multiple steps in network feature analysis, gene set over-representation analysis

Summary of scripts for running GWIS and collecting results

find_probes.py

python scripts/find_probes.py test/config_test.py

A thin wrapper to apply GWIS and PLINK to all datasets

gwas2graph.py

python scripts/gwas2graph.py test/config_test.py

reads in results from all GWIS tests and produces a JSON file.