Fixed issue that caused some interval mapping results to be wrong; the cause seems to be related to some strains being renamed in the genofiles

Added a message to the Add to Collection page warning users that anonymous collections will only be stored for 5 days

Updated genofiles

3 files changed, 15 insertions, 10 deletions

diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index c80fcb65..8df9939e 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -52,6 +52,10 @@ class webqtlCaseData(object):
             str += " variance=%2.3f" % self.variance
         if self.num_cases != None:
             str += " ndata=%d" % self.num_cases
+        if self.name != None:
+            str += " name=%s" % self.name
+        if self.name2 != None:
+            str += " name2=%s" % self.name2
         return str
 
     @property
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index a8324442..89af856e 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -47,8 +47,6 @@ class MarkerRegression(object):
 
         helper_functions.get_species_dataset_trait(self, start_vars)
 
-        #tempdata = temp_data.TempData(temp_uuid)
-
         self.temp_uuid = temp_uuid #needed to pass temp_uuid to gn1 mapping code (marker_regression_gn1.py)
 
         self.json_data = {}
@@ -59,11 +57,11 @@ class MarkerRegression(object):
 
         all_samples_ordered = self.dataset.group.all_samples_ordered()
         primary_sample_names = list(all_samples_ordered)
-
+        
         for sample in self.dataset.group.samplelist:
             in_trait_data = False
             for item in self.this_trait.data:
-                if self.this_trait.data[item].name2 == sample:
+                if self.this_trait.data[item].name == sample:
                     value = start_vars['value:' + self.this_trait.data[item].name]
                     self.samples.append(self.this_trait.data[item].name)
                     self.vals.append(value)
@@ -280,7 +278,6 @@ class MarkerRegression(object):
 
             # print("json_data:", self.json_data)
 
-
             self.js_data = dict(
                 result_score_type = self.score_type,
                 json_data = self.json_data,
@@ -657,16 +654,15 @@ class MarkerRegression(object):
             genotype = genotype.addinterval()
 
         samples, values, variances, sample_aliases = self.this_trait.export_informative()
-
+        
         trimmed_samples = []
         trimmed_values = []
         for i in range(0, len(samples)):
-            if self.this_trait.data[samples[i]].name2 in self.dataset.group.samplelist:
-                trimmed_samples.append(sample_aliases[i])
+            #if self.this_trait.data[samples[i]].name2 in self.dataset.group.samplelist:
+            if self.this_trait.data[samples[i]].name in self.samples:
+                trimmed_samples.append(samples[i])
                 trimmed_values.append(values[i])
 
-        #print("THE SAMPLES:", trimmed_samples)
-
         if self.num_perm < 100:
             self.suggestive = 0
             self.significant = 0
@@ -706,6 +702,8 @@ class MarkerRegression(object):
                                                             control = control_geno,
                                                             nboot = self.num_bootstrap)
         else:
+            # reaper_results = genotype.regression(strains = self.samples,
+                                                 # trait = self.vals)
             reaper_results = genotype.regression(strains = trimmed_samples,
                                                  trait = trimmed_values)
 
diff --git a/wqflask/wqflask/templates/collections/add.html b/wqflask/wqflask/templates/collections/add.html
index f4a69423..c5598e84 100644
--- a/wqflask/wqflask/templates/collections/add.html
+++ b/wqflask/wqflask/templates/collections/add.html
@@ -23,6 +23,9 @@
                 <input type="text" name="new_collection" placeholder="Name of new collection..."
                     data-trigger="change" data-minlength="5" data-maxlength="50">
                 <span class="help-block">Type the name of the new collection.</span>
+                {% if uc is not defined %}
+                <span class="help-block" style="color:red;">This collection will be saved to this computer for 5 days.</span>
+                {% endif %}
                 <button type="submit" name="create_new" class="btn">Create and add traits</button>
             </fieldset>