From 04136ee53bc1b240583e2af68f534cd81d31a5af Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 2 Oct 2014 21:07:49 +0000
Subject: Fixed an error when there's no locus for mRNA expression traits

---
 wqflask/base/trait.py                                   | 3 +++
 wqflask/wqflask/show_trait/show_trait.py                | 4 ++--
 wqflask/wqflask/templates/show_trait_mapping_tools.html | 4 ++--
 3 files changed, 7 insertions(+), 4 deletions(-)

(limited to 'wqflask')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 71691899..6d070d54 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -408,6 +408,7 @@ class GeneralTrait(object):
                     #self.cursor.execute(query)
                     #trait_qtl = self.cursor.fetchone()
                     if trait_qtl:
+                        print("trait_qtl:", trait_qtl)
                         self.locus, self.lrs, self.pvalue, self.mean = trait_qtl
                         print("self.locus:", self.locus)
                         if self.locus:
@@ -421,6 +422,8 @@ class GeneralTrait(object):
                             if result:
                                 self.locus_chr = result[0]
                                 self.locus_mb = result[1]
+                        else:
+                            self.locus = self.locus_chr = self.locus_mb = ""
                     else:
                         self.locus = self.locus_chr = self.locus_mb = self.lrs = self.pvalue = self.mean = ""
 
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 833c3b06..d38da8e8 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -92,7 +92,7 @@ class ShowTrait(object):
 
         #Get nearest marker for composite mapping
 
-        if self.dataset.type != "Geno" and self.dataset.type != "Publish":
+        if self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
             self.nearest_marker1 = get_nearest_marker(self.this_trait, self.dataset)[0]
             self.nearest_marker2 = get_nearest_marker(self.this_trait, self.dataset)[1]
 
@@ -109,7 +109,7 @@ class ShowTrait(object):
         hddn['suggestive'] = 0
         hddn['num_perm'] = 0
         hddn['manhattan_plot'] = False
-        if self.dataset.type != "Geno" and self.dataset.type != "Publish":
+        if self.this_trait.locus_chr != "" and self.dataset.type != "Geno" and self.dataset.type != "Publish":
             hddn['control_marker'] = self.nearest_marker1+","+self.nearest_marker2
         else:
             hddn['control_marker'] = ""
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index d6426f0c..299c3e0c 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -13,7 +13,7 @@
                     <a href="#rqtl_geno" data-toggle="tab">rqtl</a>
                 </li>
                 {% if dataset.group.species == 'human' %}
-                <li>
+                <li>self.this_trait.locus_chr != "" and 
                     <a href="#plink" data-toggle="tab">PLINK</a>
                 </li>
                 <li>
@@ -209,7 +209,7 @@
                     <div class="control-group">
                         <label for="control_rqtl_geno" class="control-label">Control Marker(s)</label>
                         <div class="controls">
-                            {% if dataset.type == 'ProbeSet' %}
+                            {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
                             <input name="control_rqtl_geno" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" />
                             {% else %}
                             <input name="control_rqtl_geno" value="" type="text" />
-- 
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