Inital python code to do PheWAS analysis from R

1 files changed, 40 insertions, 0 deletions

diff --git a/wqflask/wqflask/phewas/phewas.py b/wqflask/wqflask/phewas/phewas.py
new file mode 100644
index 00000000..399e056c
--- /dev/null
+++ b/wqflask/wqflask/phewas/phewas.py
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+# PheWAS analysis for GN2
+# Author / Maintainer: Li Hao & Danny Arends <Danny.Arends@gmail.com>
+import sys
+from numpy import *
+import scipy as sp                            # SciPy
+import rpy2.robjects as ro                    # R Objects
+import rpy2.rinterface as ri
+
+from base.webqtlConfig import GENERATED_IMAGE_DIR
+from utility import webqtlUtil                # Random number for the image
+from utility import genofile_parser           # genofile_parser
+
+import base64
+import array
+import csv
+import itertools
+
+from base import data_set
+from base import trait as TRAIT
+
+from utility import helper_functions
+from utility.tools import locate
+
+from rpy2.robjects.packages import importr
+utils = importr("utils")
+
+class PheWAS(object):
+    def __init__(self):
+        print("Initialization of PheWAS")
+        print("Initialization of PheWAS done !")
+
+    def run_analysis(self, requestform):
+        print("Starting PheWAS analysis on dataset")
+        print("Initialization of PheWAS done !")
+
+    def process_results(self, results):
+        print("Processing PheWAS output")
+        template_vars = {}
+        return(dict(template_vars))
+