Location range feature should work for correlations now, though the interface appearance needs to be improved

2 files changed, 49 insertions, 4 deletions

diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 6a120325..63a7a555 100755
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -110,6 +110,17 @@ class CorrelationResults(object):
                 self.min_expr = float(start_vars['min_expr'])
             self.p_range_lower = float(start_vars['p_range_lower'])
             self.p_range_upper = float(start_vars['p_range_upper'])
+            self.min_location_chr = start_vars['min_loc_chr']
+            self.max_location_chr = start_vars['max_loc_chr']
+            if start_vars['min_loc_mb'].isdigit():
+                self.min_location_mb = start_vars['min_loc_mb']
+            else:
+                self.min_location_mb = 0
+            if start_vars['max_loc_mb'].isdigit():
+                self.max_location_mb = start_vars['max_loc_mb']
+            else:
+                self.max_location_mb = 1000
+            self.max_location = [start_vars['max_loc_chr'], start_vars['max_loc_mb']]
             self.get_formatted_corr_type()
             self.return_number = int(start_vars['corr_return_results'])
 
@@ -167,15 +178,35 @@ class CorrelationResults(object):
                                                                        key=lambda t: -abs(t[1][0])))
 
 
+            #ZS: Convert min/max chromosome to an int for the location range option
+            min_chr_as_int = 1
+            max_chr_as_int = 30 #Just to make sure all are included if user inputs nothing
+            for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+                if chr_info.name == self.min_location_chr:
+                    min_chr_as_int = order_id
+                if chr_info.name == self.max_location_chr:
+                    max_chr_as_int = order_id
+
             for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
                 print("trait name:", trait)
                 trait_object = GeneralTrait(dataset=self.target_dataset, name=trait, get_qtl_info=True)
-                print("trait_object.mean:", trait_object.mean)
-                print("self.min_expr:", self.min_expr)
-                print("self.p_range_upper:", self.p_range_upper)
+                
+                #ZS: Convert trait chromosome to an int for the location range option
+                chr_as_int = 0
+                for order_id, chr_info in self.dataset.species.chromosomes.chromosomes.iteritems():
+                    if chr_info.name == trait_object.chr: 
+                        chr_as_int = order_id
+
                 if (float(trait_object.mean) > self.min_expr and 
                     float(self.correlation_data[trait][0]) > self.p_range_lower and
-                    float(self.correlation_data[trait][0]) < self.p_range_upper):
+                    float(self.correlation_data[trait][0]) < self.p_range_upper and
+                    chr_as_int >= min_chr_as_int and
+                    chr_as_int <= max_chr_as_int):
+    
+                    if (chr_as_int == min_chr_as_int and float(trait_object.mb) < float(self.min_location_mb)):
+                        continue
+                    elif (chr_as_int == max_chr_as_int and float(trait_object.mb) > float(self.max_location_mb)):
+                        continue
 
                     (trait_object.sample_r,
                     trait_object.sample_p,
diff --git a/wqflask/wqflask/templates/show_trait_calculate_correlations.html b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
index cefe9763..65b9d08e 100755
--- a/wqflask/wqflask/templates/show_trait_calculate_correlations.html
+++ b/wqflask/wqflask/templates/show_trait_calculate_correlations.html
@@ -80,6 +80,20 @@
             </div>
         </div>
         <div class="form-group">
+            <label class="col-xs-1 control-label">Location</label>
+            <div class="col-xs-4 controls">
+                <span style="margin:10px;">
+                Min Chr: <input name="min_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">
+                Mb: <input name="min_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
+                </span>
+                <br>
+                <span style="margin:10px;">
+                Max Chr: <input name="max_loc_chr" value="" type="text" class="form-control" style="width: 50px; display: inline;">
+                Mb: <input name="max_loc_mb" value="" type="text" class="form-control" style="width: 50px; display: inline;">
+                </span>
+            </div>
+        </div>
+        <div class="form-group">
             <label class="col-xs-1 control-label">Range</label>
             <div class="col-xs-3 controls">
                 <input name="p_range_lower" value="" type="hidden">