Begun adding pair scan option, fixed bug if no closest markers found

4 files changed, 82 insertions, 46 deletions

diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 9a3ff073..db92e14c 100755
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -65,6 +65,7 @@ class MarkerRegression(object):
             self.manhattan_plot = True
         else:
             self.manhattan_plot = False
+
         self.maf = start_vars['maf'] # Minor allele frequency
         self.suggestive = ""
         self.significant = ""
@@ -82,6 +83,12 @@ class MarkerRegression(object):
                 self.num_perm = start_vars['num_perm']
             self.control = start_vars['control_marker']
 
+            if start_vars['pair_scan'] == "true":
+                self.pair_scan = True
+            else:
+                self.pair_scan = False
+            print("pair scan:", self.pair_scan)
+
             print("DOING RQTL GENO")
             qtl_results = self.run_rqtl_geno()
             print("qtl_results:", qtl_results)
@@ -277,6 +284,7 @@ class MarkerRegression(object):
 
         ## Get pointers to some R/qtl functions
         scanone         = ro.r["scanone"]               # Map the scanone function
+        scantwo         = ro.r["scantwo"]               # Map the scantwo function
         calc_genoprob   = ro.r["calc.genoprob"]         # Map the calc.genoprob function
         read_cross      = ro.r["read.cross"]            # Map the read.cross function
         write_cross     = ro.r["write.cross"]           # Map the write.cross function
@@ -300,20 +308,31 @@ class MarkerRegression(object):
 
         # Scan for QTLs
         covar = self.create_covariates(cross_object)
-        if(r_sum(covar)[0] > 0):
-            print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar)
-        else:
-            print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno")
 
-        if int(self.num_perm) > 0:                                                                      # Do permutation (if requested by user)
+        if self.pair_scan:
+            if(r_sum(covar)[0] > 0):
+                print("Using covariate"); result_data_frame = scantwo(cross_object, pheno = "the_pheno", addcovar = covar)
+            else:
+                print("No covariates"); result_data_frame = scantwo(cross_object, pheno = "the_pheno")
+ 
+            print("pair scan results:", result_data_frame)
+
+            return 0
+        else:
             if(r_sum(covar)[0] > 0):
-                perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = int(self.num_perm))
+                print("Using covariate"); result_data_frame = scanone(cross_object, pheno = "the_pheno", addcovar = covar)
             else:
-                perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = int(self.num_perm))
+                print("No covariates"); result_data_frame = scanone(cross_object, pheno = "the_pheno")
+
+            if int(self.num_perm) > 0:                                                                      # Do permutation (if requested by user)
+                if(r_sum(covar)[0] > 0):
+                    perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", addcovar = covar, n_perm = int(self.num_perm))
+                else:
+                    perm_data_frame = scanone(cross_object, pheno_col = "the_pheno", n_perm = int(self.num_perm))
 
-            self.process_rqtl_perm_results(perm_data_frame)                                             # Functions that sets the thresholds for the webinterface
+                self.process_rqtl_perm_results(perm_data_frame)                                             # Functions that sets the thresholds for the webinterface
 
-        return self.process_rqtl_results(result_data_frame)
+            return self.process_rqtl_results(result_data_frame)
 
     def add_phenotype(self, cross, pheno_as_string):
         ro.globalenv["the_cross"] = cross
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 62411640..11fd2644 100755
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1310,6 +1310,9 @@ def get_nearest_marker(this_trait, this_db):
     result = g.db.execute(query).fetchall()
     print("result:", result)
 
-    return result[0][0], result[1][0]
+    if result == []:
+        return "", ""
+    else:
+        return result[0][0], result[1][0]
     
     
diff --git a/wqflask/wqflask/templates/show_trait_mapping_tools.html b/wqflask/wqflask/templates/show_trait_mapping_tools.html
index d6c7b18e..946dab49 100755
--- a/wqflask/wqflask/templates/show_trait_mapping_tools.html
+++ b/wqflask/wqflask/templates/show_trait_mapping_tools.html
@@ -80,19 +80,31 @@
                 </div>
                 
                 <div class="tab-pane" id="pylmm">
+                    
                     <div style="padding: 20px" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
-                            <label for="mapping_permutations" class="col-xs-1 control-label">Permutations</label>
-                            <div style="margin-left: 20px;" class="col-xs-2 controls">
-                                <input name="num_perm_pylmm" value="0" type="text" class="form-control">
+                            <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                                <input name="num_pylmm" value="2000" type="text" class="form-control">
                             </div>
                         </div>
                         <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
                             Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label class="col-xs-1 control-label">Manhattan Plot</label>
-                            <div style="margin-left:20px;" class="col-xs-4 controls">                      
+                            <label for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                                {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
+                                <input name="control_pylmm" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" />
+                                {% else %}
+                                <input name="control_pylmm" value="" type="text" />
+                                {% endif %}
+                            </div>
+                        </div>
+
+                        <div class="mapping_method_fields form-group">
+                            <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+                            <div class="col-xs-12 controls">                      
                                 <label class="radio-inline">
                                     <input type="radio" name="manhattan_plot_pylmm" value="true">
                                     Yes
@@ -103,39 +115,30 @@
                                </label>
                             </div>
                         </div>
-                        <!--<div class="form-group" id="suggestive">
-                            <label for="suggestive_reaper" class="control-label" title="Control Locus">LOD score greater than: </label>
-                            <div class="controls">
-                                <input name="suggestive_reaper" type="text" value="0" class="form-control">
+                        <div class="form-group">
+                            <div style="padding-left:15px;" class="controls">
+                                <button id="pylmm_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+                                    <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+                                </button>
                             </div>
-                        </div>-->
-                    </div>
-                    
-                    <div class="form-group">
-                        <label for="marker_regression_submit" class="col-xs-1 control-label"></label>
-                        <div style="margin-left:20px;" class="col-xs-4 controls">
-                            <button id="pylmm_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
-                                Compute
-                            </button>
                         </div>
                     </div>
-
                 </div>
                 <div class="tab-pane" id="rqtl_geno">
                     
                     <div style="padding: 20px" class="form-horizontal">
                         <div class="mapping_method_fields form-group">
-                            <label for="mapping_permutations" class="col-xs-1 control-label">Permutations</label>
-                            <div style="margin-left: 20px;" class="col-xs-2 controls">
-                                <input name="num_perm_rqtl_geno" value="500" type="text" class="form-control">
+                            <label for="mapping_permutations" class="col-xs-2 control-label">Permutations</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
+                                <input name="num_perm_rqtl_geno" value="2000" type="text" class="form-control">
                             </div>
                         </div>
                         <div id="permutations_alert" class="alert alert-error alert-warning" style="display:none;">
                             Please be aware that permutations can take a very long time (~20 minutes for 500 permutations)
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label for="mapping_permutations" class="col-xs-1 control-label">Control&nbsp;for</label>
-                            <div style="margin-left: 20px;" class="col-xs-2 controls">
+                            <label for="control_for" class="col-xs-2 control-label">Control&nbsp;for</label>
+                            <div style="margin-left: 20px;" class="col-xs-4 controls">
                                 {% if dataset.type == 'ProbeSet' and this_trait.locus_chr != "" %}
                                 <input name="control_rqtl_geno" value="{{ nearest_marker1+","+nearest_marker2 }}" type="text" />
                                 {% else %}
@@ -144,8 +147,8 @@
                             </div>
                         </div>
                         <div class="mapping_method_fields form-group">
-                            <label class="col-xs-1 control-label">Manhattan&nbsp;Plot</label>
-                            <div style="margin-left:35px;" class="col-xs-4 controls">                      
+                            <label style="text-align:left;" class="col-xs-12 control-label">Manhattan Plot</label>
+                            <div class="col-xs-12 controls">                      
                                 <label class="radio-inline">
                                     <input type="radio" name="manhattan_plot_rqtl" value="true">
                                     Yes
@@ -156,17 +159,27 @@
                                </label>
                             </div>
                         </div>
-                    </div>
-                    
-                    <div class="form-group">
-                        <label for="marker_regression_submit" class="col-xs-1 control-label"></label>
-                        <div style="margin-left:20px;" class="col-xs-4 controls">
-                            <button id="rqtl_geno_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
-                                <i class="icon-ok-circle icon-white"></i> Compute
-                            </button>
+                        <div class="mapping_method_fields form-group">
+                            <label style="text-align:left;" class="col-xs-12 control-label">Pair Scan</label>
+                            <div class="col-xs-12 controls">                      
+                                <label class="radio-inline">
+                                    <input type="radio" name="pair_scan" value="true">
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="pair_scan" value="false" checked="">
+                                    No
+                               </label>
+                            </div>
+                        </div>
+                        <div class="form-group">
+                            <div style="padding-left:15px;" class="controls">
+                                <button id="rqtl_geno_compute" class="btn submit_special btn-primary" data-url="/marker_regression" title="Compute Marker Regression">
+                                    <i class="icon-ok-circle icon-white"></i> Open Mapping Tool
+                                </button>
+                            </div>
                         </div>
                     </div>
-       
                 </div>
                 
                 {% if dataset.group.species == 'human' %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 9110c5a1..e60852d5 100755
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -285,7 +285,8 @@ def marker_regression_page():
         'maf',
         'manhattan_plot',
         'control_marker',
-        'control_marker_db'
+        'control_marker_db',
+        'pair_scan'
     )
 
     start_vars = {}