GenoWAP (Deprecated! See here for the newest version)

Post-GWAS Prioritization through Integrated Analysis of Functional Annotation

Dependencies

• python version >=3.4 or >=2.7,6
• requests
• progressbar2
• scipy
• numpy

To install these packages, you can conveniently use pip. For example,

pip install numpy

or

pip install --user numpy

Python2 vs. Python3

prioritize2.py is the python2 compatible version, and prioritize3.py is the python3 version. The latter version has slightly better precision (14 vs 18 digits after decimal point)

Usage

GenoWAP [-h] [-o DESTINATION_PATH] [-b NBINS] [-t THRESHOLD] [-a ANNOTATION_PATH] GWAS_DATA_PATH

When ANNOTATION_PATH is not specified, GenoWAP tries to download data from GenoCanyon, and save to file "temp.data" in the current directory. See GenoWAP -h for more detail

DATA Format

The following format is for both GWAS_DATA and ANNOTATION:

A text file with n lines, each line contains chromosome number, coordinate and the GWAS p-value, separated by one tab (i.e. '\t')

Note: the data given is assumed to contain no duplicated entries. If it does, then the duplicated entries will be ignored during computation and removed from output.

Build

freeze.py is used for building executables. Please use cx_Freeze for the build:

1. Make sure all dependencies are installed for the preferred python version with which you wish to run GenoWAP.

2. Rename the correct python source code to GenoWAP.py

3. Run (where python points to the preferred version of python):

python freeze.py build

The executable will be named GenoWAP under the build directory.