From f09f6ffa285ad0aa7280dbadaa4eb8f0686d329f Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Wed, 9 Jan 2013 14:57:25 -0600
Subject: Got the marker regression page to display again

Passed lrs_array values as js_data for the permutation histogram
---
 .../wqflask/marker_regression/marker_regression.py | 22 ++++++++---------
 wqflask/wqflask/templates/marker_regression.html   | 28 ----------------------
 2 files changed, 11 insertions(+), 39 deletions(-)

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 73f1246f..615f6f77 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -52,9 +52,12 @@ class MarkerRegression(object):
         #if not self.openMysql():
         #    return
 
-        print("start_vars are: ", pf(start_vars))
+        #print("start_vars are: ", pf(start_vars))
 
         self.dataset = create_dataset(start_vars['dataset_name'])
+        self.this_trait = GeneralTrait(dataset=self.dataset.name,
+                                       name=start_vars['trait_id'],
+                                       cellid=None)        
         self.num_perm = int(start_vars['num_perm'])
 
         # Passed in by the form (user might have edited)
@@ -82,10 +85,6 @@ class MarkerRegression(object):
                 self.vals.append(float(value))
                 self.variances.append(variance)
 
-        print("self.samples is:", pf(self.samples))
-        print("self.vals is:", pf(self.vals))
-        print("self.variances is:", pf(self.variances))
-
         #self.initializeParameters(start_vars)
 
         #filename= webqtlUtil.genRandStr("Itvl_")
@@ -305,9 +304,11 @@ class MarkerRegression(object):
             # end: common part with human data
             
             self.js_data = dict(
-                qtl_results = self.pure_qtl_results,
-                #lrs_array = vars(self.lrs_array),
+                #qtl_results = self.pure_qtl_results,
+                lrs_array = self.lrs_array,
             )
+            
+            print("bears self.js_data is: ", pf(self.js_data))
 
 
 
@@ -480,8 +481,8 @@ class MarkerRegression(object):
                 if result.lrs > self.lrs_thresholds.suggestive:
                     suggestive_results.append(result)
             filtered_results = suggestive_results 
-        
-        
+
+
         # Todo (2013): Use top_10 variable to generate page message about whether top 10 was used
         if not filtered_results:
             # We use the 10 results with the highest LRS values
@@ -489,8 +490,7 @@ class MarkerRegression(object):
             self.top_10 = True
         else:
             self.top_10 = False
-            
-            
+
 
 
         #qtlresults2 = []
diff --git a/wqflask/wqflask/templates/marker_regression.html b/wqflask/wqflask/templates/marker_regression.html
index db2de604..2fe20fb0 100644
--- a/wqflask/wqflask/templates/marker_regression.html
+++ b/wqflask/wqflask/templates/marker_regression.html
@@ -11,34 +11,6 @@
         </div>
     </header>
 
-    <dl class="dl-horizontal">
-        <dt>Aliases</dt>
-        <dd>{{ this_trait.alias_fmt }}</dd>
-    
-        <dt>Location</dt>
-        <dd>{{ this_trait.location_fmt }}</dd>
-    
-        <dt>Database</dt>
-        <dd>
-            <a href="{{ url_for('static', filename='/dbdoc/' + dataset.fullname + '.html') }}" target="_blank">
-                {{ dataset.name }}
-            </a>
-        </dd>
-    
-        {% if this_trait.probe_set_specificity %}
-        <dt>
-            <a href="/blatInfo.html" target="_blank"
-               title="Values higher than 2 for the specificity are good">
-                BLAT Specifity
-            </a>
-        </dt>
-        <dd>{{ "%.1f" % (this_trait.probe_set_specificity) }}</dd>
-        {% endif %}
-        {% if this_trait.probe_set_blat_score %}
-        <dt>BLAT Score</dt>
-        <dd>{{ "%i" % (this_trait.probe_set_blat_score) }}</dd>
-        {% endif %}
-    </dl>
 
     <!-- End of body -->
 
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