From 5a3f413da480123e3ad943b5f556e0a557f185cc Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Thu, 9 May 2013 22:54:34 +0000
Subject: Just added some print statements so I can show matrix/vector shapes
 to Tony

---
 wqflask/base/data_set.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1520b180..d7328441 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -385,7 +385,7 @@ class PhenotypeDataSet(DataSet):
                 continue   # for now
                 if not webqtlUtil.hasAccessToConfidentialPhenotypeTrait(privilege=self.privilege, userName=self.userName, authorized_users=this_trait.authorized_users):
                     description = this_trait.pre_publication_description
-            this_trait.description_display = description
+            this_trait.description_display = unicode(description, "utf8")
 
             if not this_trait.year.isdigit():
                 this_trait.pubmed_text = "N/A"
-- 
cgit v1.2.3


From 43eb99c11d8ef371bba926a3a63bf599b56820ae Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Fri, 31 May 2013 16:01:31 +0000
Subject: Fixed the location column for the quick search page

Began writing some jquery to automatically open the first tab
within each species tab on the quick search page (not done yet)
---
 wqflask/base/trait.py                       |   2 +-
 wqflask/wqflask/my_pylmm/pyLMM/lmm.py       |   2 +
 wqflask/wqflask/templates/quick_search.html | 110 ++--------------------------
 wqflask/wqflask/views.py                    |   2 +-
 4 files changed, 12 insertions(+), 104 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7c1c035c..dde8b8d8 100755
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -302,7 +302,7 @@ class GeneralTrait:
 
             #XZ: assign SQL query result to trait attributes.
             for i, field in enumerate(self.dataset.display_fields):
-                setattr(self, field, traitInfo[i])
+                setattr(self, field, str(traitInfo[i]))
 
             if self.dataset.type == 'Publish':
                 self.confidential = 0
diff --git a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
index 62fb0fbd..5bfc3a01 100644
--- a/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
+++ b/wqflask/wqflask/my_pylmm/pyLMM/lmm.py
@@ -243,6 +243,8 @@ def run(pheno_vector,
     with Bench("LMM_ob fitting"):
         lmm_ob.fit()
 
+    print("genotype_matrix: ", genotype_matrix.shape)
+
     with Bench("Doing GWAS"):
         t_stats, p_values = GWAS(pheno_vector,
                                 genotype_matrix,
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index 5877a840..01588924 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -105,7 +105,7 @@
                                         {% if result.result_fields['species'] == species %}
                                         <tr>
                                             <td>
-                                                <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
+                                                <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}">
                                                    {{ result.result_fields['name'] }}
                                                 </a>
                                             </td>
@@ -114,7 +114,7 @@
                                             <td>{{ result.result_fields['dataset_name'] }}</td>
                                             <td>{{ result.result_fields['symbol'] }}</td>
                                             <td>{{ result.result_fields['description'] }}</td>
-                                            <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
+                                            <td>Chr {{ result.result_fields['chr'] }}: {{ result.result_fields['mb'] }}</td>
                                             <td>{{ result.result_fields['mean'] }}</td>
                                             <td>{{ result.result_fields['lrs'] }}</td>
                                         </tr>
@@ -168,105 +168,6 @@
 
 {% endblock %}
 
-                {#
-                    <table id="pheno_results" class="table table-hover table-striped table-bordered">
-                        <thead>
-                            <tr>
-                            <th>Id</th>
-                            <th>Species</th>
-                            <th>Group</th>
-                            <th>Description</th>
-                            <th>LRS</th>
-                            <th>Year</th>
-                            <th>Authors</th>
-                            </tr>
-                        </thead>
-                        <tbody>
-                            {% for result in results.phenotype %}
-                            <tr>
-                                <td>{{ result.result_fields['phenotype_id'] }}</td>
-                                <td>{{ result.result_fields['species'] }}</td>
-                                <td>{{ result.result_fields['group_name'] }}</td>
-                                <td>{{ result.result_fields['description'] }}</td>
-                                <td>{{ result.result_fields['lrs'] }}</td>
-                                <td>
-                                    <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
-                                        {{ result.result_fields['year'] }}
-                                    </a>
-                                </td>
-                                <td>{{ result.result_fields['authors'] }}</td>
-                            </tr>
-                            {% endfor %}
-                        </tbody>
-                    </table>
-                </div>
-                <div class="tab-pane" id="tab2">
-                    <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
-                        <thead>
-                            <tr>
-                            <th>Record ID</th>
-                            <th>Species</th>
-                            <th>Group</th>
-                            <th>Data Set</th>
-                            <th>Symbol</th>
-                            <th>Description</th>
-                            <th>Location</th>
-                            <th>Mean Expr</th>
-                            <th>Max LRS</th>
-                            </tr>
-                        </thead>
-                        <tbody>
-                            {% for result in results.mrna_assay %}
-                            <tr>
-                                <td>
-                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
-                                       {{ result.result_fields['name'] }}
-                                    </a>
-                                </td>
-                                <td>{{ result.result_fields['species'] }}</td>
-                                <td>{{ result.result_fields['group_name'] }}</td>
-                                <td>{{ result.result_fields['dataset_name'] }}</td>
-                                <td>{{ result.result_fields['symbol'] }}</td>
-                                <td>{{ result.result_fields['description'] }}</td>
-                                <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
-                                <td>{{ result.result_fields['mean'] }}</td>
-                                <td>{{ result.result_fields['lrs'] }}</td>
-                            </tr>
-                            {% endfor %}
-                        </tbody>
-                    </table>                    
-                </div>
-                <div class="tab-pane" id="tab3">
-                    <table id="geno_results" class="table table-hover table-striped table-bordered">
-                        <thead>
-                            <tr>
-                            <th>Marker</th>
-                            <th>Species</th>
-                            <th>Group</th>
-                            <th>Data Set</th>
-                            <th>Location</th>
-                            </tr>
-                        </thead>
-                        <tbody>
-                            {% for result in results.genotype %}
-                            <tr>
-                                <td>
-                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
-                                        {{ result.result_fields['marker_name'] }}
-                                    </a>
-                                </td>
-                                <td>{{ result.result_fields['species'] }}</td>
-                                <td>{{ result.result_fields['group_name'] }}</td>
-                                <td>{{ result.result_fields['dataset_name'] }}</td>
-                                <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
-                            </tr>
-                            {% endfor %}
-                        </tbody>
-                    </table>                     
-                </div>
-                #}
-
-
 {% block js %}  
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
@@ -274,9 +175,14 @@
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 
-    
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
+            
+            $("div[id^='tab'").bind('click', function(){
+                tab_id = $(this).attr('id');
+                $("a[href^='"+tab_id+"']").first().trigger('click');
+            });
+            
             $('#species_level ul li:first').addClass('active');
             $('#trait_type_level ul li:first').addClass('active');
             console.time("Creating table");
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 1af324b2..4480e8da 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -80,7 +80,7 @@ def search_page():
         print("key is:", pf(key))
         with Bench("Loading cache"):
             result = Redis.get(key)
-
+            
         if result:
             print("Cache hit!!!")
             with Bench("Loading results"):
-- 
cgit v1.2.3


From 7938d8c6cbdfe866ebf9ec62dec0fe5c43cf2d6f Mon Sep 17 00:00:00 2001
From: Zachary Sloan
Date: Wed, 12 Jun 2013 22:45:57 +0000
Subject: Fixed a couple issues with the template that caused the regular
 search results and show trait page to not display

---
 wqflask/base/data_set.py                          |   4 +-
 wqflask/wqflask/search_results.py                 |  59 +++++----
 wqflask/wqflask/templates/index_page.html         |   9 +-
 wqflask/wqflask/templates/quick_search.html       | 146 ++++++++++++++++++----
 wqflask/wqflask/templates/show_trait_details.html |   4 +-
 5 files changed, 165 insertions(+), 57 deletions(-)

(limited to 'wqflask/base')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index d7328441..9b0a3dcc 100755
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -735,8 +735,10 @@ class MrnaAssayDataSet(DataSet):
             trait_location_value = 1000000
 
             if this_trait.chr and this_trait.mb:
+                print("this_trait.chr is:", this_trait.chr)
+                print("this_trait.mb is:", this_trait.mb)
                 try:
-                    trait_location_value = int(this_trait.chr)*1000 + this_trait.mb
+                    trait_location_value = float(this_trait.chr)*1000 + float(this_trait.mb)
                 except:
                     if this_trait.chr.upper() == 'X':
                         trait_location_value = 20*1000 + this_trait.mb
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index ad74f6cc..63aa481e 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -42,7 +42,7 @@ from utility import formatting
     #def __init__(self, key, result_fields):
     #    self.key = key
     #    self.result_fields = result_fields
-
+    
 
 class SearchResultPage(object):
     #maxReturn = 3000
@@ -73,6 +73,7 @@ class SearchResultPage(object):
             self.quick = True
             self.search_terms = kw['q']
             print("self.search_terms is: ", self.search_terms)
+            self.trait_type = kw['trait_type']
             self.quick_search()
         else:
             self.results = []
@@ -91,7 +92,7 @@ class SearchResultPage(object):
 
         """
         self.trait_list = []
-
+        
         species = webqtlDatabaseFunction.retrieve_species(self.dataset.group.name)
         
         # result_set represents the results for each search term; a search of 
@@ -100,7 +101,7 @@ class SearchResultPage(object):
         for result in self.results:
             if not result:
                 continue
-
+            
             #### Excel file needs to be generated ####
 
             print("foo locals are:", locals())
@@ -123,42 +124,46 @@ class SearchResultPage(object):
                     FROM QuickSearch
                     WHERE MATCH (terms)
                           AGAINST ('{}' IN BOOLEAN MODE) """.format(search_terms)
-        #print("query is: ", query)
         
         with Bench("Doing QuickSearch Query: "):
             dbresults = g.db.execute(query, no_parameters=True).fetchall()
         #print("results: ", pf(results))
-
+        
         self.results = collections.defaultdict(list)
-
+        
         type_dict = {'PublishXRef': 'phenotype',
                    'ProbeSetXRef': 'mrna_assay',
                    'GenoXRef': 'genotype'}
-
+        
         self.species_groups = {}
+        
         for dbresult in dbresults:
             this_result = {}
             this_result['table_name'] = dbresult.table_name
-            this_result['key'] = dbresult.the_key
-            this_result['result_fields'] = json.loads(dbresult.result_fields)
-            this_species = this_result['result_fields']['species']
-            this_group = this_result['result_fields']['group_name']
-            if this_species not in self.species_groups:
-                self.species_groups[this_species] = {}
-            if type_dict[dbresult.table_name] not in self.species_groups[this_species]:
-                self.species_groups[this_species][type_dict[dbresult.table_name]] = []
-            if this_group not in self.species_groups[this_species][type_dict[dbresult.table_name]]:
-                self.species_groups[this_species][type_dict[dbresult.table_name]].append(this_group)
-            #if type_dict[dbresult.table_name] not in self.species_groups:
-            #    self.species_groups[type_dict[dbresult.table_name]] = {}
-            #if this_species not in self.species_groups[type_dict[dbresult.table_name]]:
-            #    self.species_groups[type_dict[dbresult.table_name]][this_species] = []
-            #if this_group not in self.species_groups[type_dict[dbresult.table_name]][this_species]:
-            #    self.species_groups[type_dict[dbresult.table_name]][this_species].append(this_group)
-            self.results[type_dict[dbresult.table_name]].append(this_result)
-
-        #print("results: ", pf(self.results['phenotype']))
-
+            if self.trait_type == type_dict[dbresult.table_name] or self.trait_type == 'all':
+                this_result['key'] = dbresult.the_key
+                this_result['result_fields'] = json.loads(dbresult.result_fields)
+                this_species = this_result['result_fields']['species']
+                this_group = this_result['result_fields']['group_name']
+                if this_species not in self.species_groups:
+                    self.species_groups[this_species] = {}
+                if type_dict[dbresult.table_name] not in self.species_groups[this_species]:
+                    self.species_groups[this_species][type_dict[dbresult.table_name]] = []
+                if this_group not in self.species_groups[this_species][type_dict[dbresult.table_name]]:
+                    self.species_groups[this_species][type_dict[dbresult.table_name]].append(this_group)
+                #if type_dict[dbresult.table_name] not in self.species_groups:
+                #    self.species_groups[type_dict[dbresult.table_name]] = {}
+                #if this_species not in self.species_groups[type_dict[dbresult.table_name]]:
+                #    self.species_groups[type_dict[dbresult.table_name]][this_species] = []
+                #if this_group not in self.species_groups[type_dict[dbresult.table_name]][this_species]:
+                #    self.species_groups[type_dict[dbresult.table_name]][this_species].append(this_group)
+                self.results[type_dict[dbresult.table_name]].append(this_result)
+            
+        import redis
+        Redis = redis.Redis()
+        
+        
+        
     #def get_group_species_tree(self):
     #    self.species_groups = collections.default_dict(list)
     #    for key in self.results:
diff --git a/wqflask/wqflask/templates/index_page.html b/wqflask/wqflask/templates/index_page.html
index b4376ce3..a9f2cb24 100644
--- a/wqflask/wqflask/templates/index_page.html
+++ b/wqflask/wqflask/templates/index_page.html
@@ -32,7 +32,14 @@
                     </div>
                     <form method="get" action="/search"  name="SEARCHFORM">
                         <fieldset>
-                            <label for="quick">Search:</label>
+                            <div class="input-prepend">
+                                <select id="trait_type" name="trait_type" class="span2">
+                                    <option value="all">All</option>
+                                    <option value="mrna_assay">Molecular Assays</option>
+                                    <option value="phenotype">Phenotypes</option>
+                                    <option value="genotype">Genotypes</option>
+                                </select>
+                            </div>
                             <div class="input-append">
                                 <input class="input-xlarge"
                                     id="quick" name="q"
diff --git a/wqflask/wqflask/templates/quick_search.html b/wqflask/wqflask/templates/quick_search.html
index 01588924..b0e38708 100644
--- a/wqflask/wqflask/templates/quick_search.html
+++ b/wqflask/wqflask/templates/quick_search.html
@@ -26,7 +26,11 @@
             {% endif %}
         </ul>
 
-        <div id="species_level" class="tabbable"> <!-- Only required for left/right tabs -->
+
+        <div class="tabbable"> <!-- Only required for left/right tabs -->
+            {% if trait_type == 'all' %}
+                {% include 'all_results.html' %}
+            {% else %}
             <ul class="nav nav-tabs">
                 {% for species in species_groups %}
                 <li> <a href="#tab{{ loop.index }}" data-toggle="tab">{{ species }}</a></li>
@@ -34,11 +38,12 @@
             </ul>
             <div class="tab-content">
                 {% for species in species_groups %}
-                <div class="tab-pane" id="tab{{ loop.index }}">
-                    <div id="trait_type_level" class="tabbable tabs-left">
+                <div class="tab-pane active" id="tab{{ loop.index }}">
+                    <div>
+                        {#
                         <ul class="nav nav-tabs">
                             {% if species_groups[species]['phenotype'] %}
-                            <li> <a href="#tab{{ loop.index }}_1" data-toggle="tab">Phenotype</a></li>
+                            <li class="active"> <a href="#tab{{ loop.index }}_1" data-toggle="tab">Phenotype</a></li>
                             {% endif %}
                             {% if species_groups[species]['mrna_assay'] %}
                             <li> <a href="#tab{{ loop.index }}_2" data-toggle="tab">mRNA Assay</a></li>
@@ -47,9 +52,9 @@
                             <li> <a href="#tab{{ loop.index }}_3" data-toggle="tab">Genotype</a></li>
                             {% endif %}
                         </ul>
-                        <div class="tab-content">
-                            {% if species_groups[species]['phenotype'] %}
-                            <div class="tab-pane active" id="tab{{ loop.index }}_1">
+                        #}
+                        <div>
+                            {% if trait_type == 'phenotype' and species_groups[species]['phenotype'] %}
                                 <table id="pheno_results" class="table table-hover table-striped table-bordered">
                                     <thead>
                                         <tr>
@@ -82,10 +87,8 @@
                                         {% endfor %}
                                     </tbody>
                                 </table>
-                            </div>
                             {% endif %}
-                            {% if species_groups[species]['mrna_assay'] %}
-                            <div class="tab-pane" id="tab{{ loop.index }}_2">
+                            {% if trait_type == 'mrna_assay' and species_groups[species]['mrna_assay'] %}
                                 <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
                                     <thead>
                                         <tr>
@@ -105,7 +108,7 @@
                                         {% if result.result_fields['species'] == species %}
                                         <tr>
                                             <td>
-                                                <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}">
+                                                <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
                                                    {{ result.result_fields['name'] }}
                                                 </a>
                                             </td>
@@ -114,18 +117,16 @@
                                             <td>{{ result.result_fields['dataset_name'] }}</td>
                                             <td>{{ result.result_fields['symbol'] }}</td>
                                             <td>{{ result.result_fields['description'] }}</td>
-                                            <td>Chr {{ result.result_fields['chr'] }}: {{ result.result_fields['mb'] }}</td>
+                                            <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
                                             <td>{{ result.result_fields['mean'] }}</td>
                                             <td>{{ result.result_fields['lrs'] }}</td>
                                         </tr>
                                         {% endif %}
                                         {% endfor %}
                                     </tbody>
-                                </table>       
-                            </div>
+                                </table>
                             {% endif %}
-                            {% if species_groups[species]['genotype'] %}
-                            <div class="tab-pane" id="tab{{ loop.index }}_3">
+                            {% if trait_type == 'genotype' and species_groups[species]['genotype'] %}
                                 <table id="geno_results" class="table table-hover table-striped table-bordered">
                                     <thead>
                                         <tr>
@@ -153,14 +154,14 @@
                                         {% endif %}
                                         {% endfor %}
                                     </tbody>
-                                </table>   
-                            </div>
+                                </table>
                             {% endif %}
                         </div>
                     </div>
                 </div>
                 {% endfor %}
             </div>
+            {% endif %}
         </div>
     </div>
 
@@ -168,6 +169,105 @@
 
 {% endblock %}
 
+                {#
+                    <table id="pheno_results" class="table table-hover table-striped table-bordered">
+                        <thead>
+                            <tr>
+                            <th>Id</th>
+                            <th>Species</th>
+                            <th>Group</th>
+                            <th>Description</th>
+                            <th>LRS</th>
+                            <th>Year</th>
+                            <th>Authors</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {% for result in results.phenotype %}
+                            <tr>
+                                <td>{{ result.result_fields['phenotype_id'] }}</td>
+                                <td>{{ result.result_fields['species'] }}</td>
+                                <td>{{ result.result_fields['group_name'] }}</td>
+                                <td>{{ result.result_fields['description'] }}</td>
+                                <td>{{ result.result_fields['lrs'] }}</td>
+                                <td>
+                                    <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&list_uids={{ result.result_fields['pubmed_id'] }}&dopt=Abstract">
+                                        {{ result.result_fields['year'] }}
+                                    </a>
+                                </td>
+                                <td>{{ result.result_fields['authors'] }}</td>
+                            </tr>
+                            {% endfor %}
+                        </tbody>
+                    </table>
+                </div>
+                <div class="tab-pane" id="tab2">
+                    <table id="mrna_assay_results" class="table table-hover table-striped table-bordered">
+                        <thead>
+                            <tr>
+                            <th>Record ID</th>
+                            <th>Species</th>
+                            <th>Group</th>
+                            <th>Data Set</th>
+                            <th>Symbol</th>
+                            <th>Description</th>
+                            <th>Location</th>
+                            <th>Mean Expr</th>
+                            <th>Max LRS</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {% for result in results.mrna_assay %}
+                            <tr>
+                                <td>
+                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['name'] }}&dataset={{ result.result_fields['dataset'] }}"
+                                       {{ result.result_fields['name'] }}
+                                    </a>
+                                </td>
+                                <td>{{ result.result_fields['species'] }}</td>
+                                <td>{{ result.result_fields['group_name'] }}</td>
+                                <td>{{ result.result_fields['dataset_name'] }}</td>
+                                <td>{{ result.result_fields['symbol'] }}</td>
+                                <td>{{ result.result_fields['description'] }}</td>
+                                <td>{{ result.result_fields['chr'] }} : {{ result['mb'] }}</td>
+                                <td>{{ result.result_fields['mean'] }}</td>
+                                <td>{{ result.result_fields['lrs'] }}</td>
+                            </tr>
+                            {% endfor %}
+                        </tbody>
+                    </table>                    
+                </div>
+                <div class="tab-pane" id="tab3">
+                    <table id="geno_results" class="table table-hover table-striped table-bordered">
+                        <thead>
+                            <tr>
+                            <th>Marker</th>
+                            <th>Species</th>
+                            <th>Group</th>
+                            <th>Data Set</th>
+                            <th>Location</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {% for result in results.genotype %}
+                            <tr>
+                                <td>
+                                    <a href="http://gn2python.genenetwork.org/show_trait?trait_id={{ result.result_fields['marker_name'] }}&dataset={{ result.result_fields['dataset'] }}">
+                                        {{ result.result_fields['marker_name'] }}
+                                    </a>
+                                </td>
+                                <td>{{ result.result_fields['species'] }}</td>
+                                <td>{{ result.result_fields['group_name'] }}</td>
+                                <td>{{ result.result_fields['dataset_name'] }}</td>
+                                <td>{{ result.result_fields['chr'] }} : {{ result.result_fields['mb'] }}</td>
+                            </tr>
+                            {% endfor %}
+                        </tbody>
+                    </table>                     
+                </div>
+                #}
+
+
 {% block js %}  
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
     <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.dataTables.min.js"></script>
@@ -175,16 +275,9 @@
     <script language="javascript" type="text/javascript" src="/static/packages/TableTools/media/js/TableTools.min.js"></script>
     <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
 
+    
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
-            
-            $("div[id^='tab'").bind('click', function(){
-                tab_id = $(this).attr('id');
-                $("a[href^='"+tab_id+"']").first().trigger('click');
-            });
-            
-            $('#species_level ul li:first').addClass('active');
-            $('#trait_type_level ul li:first').addClass('active');
             console.time("Creating table");
             $('#pheno_results, #mrna_assay_results, #geno_results').dataTable( {
                 //"sDom": "<<'span3'l><'span3'T><'span4'f>'row-fluid'r>t<'row-fluid'<'span6'i><'span6'p>>",
@@ -210,3 +303,4 @@
         });
     </script>
 {% endblock %}
+
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index c3abfc9f..b57c3c21 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -19,11 +19,11 @@
             BLAT Specifity
         </a>
     </dt>
-    <dd>{{ "%.1f" % (this_trait.probe_set_specificity) }}</dd>
+    <dd>{{ "%s" % (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>
+    <dd>{{ "%s" % (this_trait.probe_set_blat_score) }}</dd>
     {% endif %}
 </dl>
 
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