Fixed some bugs related to getting the marker regression page working

with Nick's code

2 files changed, 8 insertions, 7 deletions

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 182e15e6..d4e97370 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -22,8 +22,10 @@
 
 from __future__ import absolute_import, print_function, division
 import os
+import math
 
 import json
+import itertools
 
 from flask import Flask, g
 
@@ -70,12 +72,9 @@ class Markers(object):
     """Todo: Build in cacheing so it saves us reading the same file more than once"""
     def __init__(self, name):
         json_data_fh = open(os.path.join(webqtlConfig.NEWGENODIR + name + '.json'))
-        self.markers = json.load(json_data)
+        self.markers = json.load(json_data_fh)
     
-    def add_pvalues(p_values):
-        #for count, marker in enumerate(self.markers):
-        #    marker['p_value'] = p_values[count]
-            
+    def add_pvalues(self, p_values):
         for marker, p_value in itertools.izip(self.markers, p_values):
             marker['p_value'] = p_value
             #Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 1d005df4..c9451154 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -458,7 +458,7 @@ class MarkerRegression(object):
         #json_data = open(os.path.join(webqtlConfig.NEWGENODIR + self.dataset.group.name + '.json'))
         #markers = json.load(json_data)
         
-        genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers]
+        genotype_data = [marker['genotypes'] for marker in self.dataset.group.markers.markers]
         
         no_val_samples = self.identify_empty_samples()
         trimmed_genotype_data = self.trim_genotypes(genotype_data, no_val_samples)
@@ -502,7 +502,9 @@ class MarkerRegression(object):
         #                                       trait = self.vals,
         #                                       nperm=self.num_perm)
 
-        self.lrs_values = [marker['lrs_value'] for marker in self.dataset.group.markers]
+        self.lrs_values = [marker['lrs_value'] for marker in self.dataset.group.markers.markers]
+        print("self.lrs_values is:", pf(self.lrs_values))
+        print("int(self.num_perm*0.37-1)", pf(int(self.num_perm*0.37-1)))
 
         self.lrs_thresholds = Bunch(
                                 suggestive = self.lrs_values[int(self.num_perm*0.37-1)],