Fixed drop-down scripts to more appropriately deal with BXD300 groups (though there's still a minor issue with a few datasets)

Added some header data to mapping output file

Fixed links in Network Group nodes/edges

5 files changed, 122 insertions, 21 deletions

diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 6553f090..1123f997 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -96,13 +96,14 @@ def get_groups(species):
         Cursor.execute("""select InbredSet.Name, InbredSet.FullName from InbredSet,
                        Species,
                        ProbeFreeze, GenoFreeze, PublishFreeze where Species.Name = '%s'
-                       and InbredSet.SpeciesId = Species.Id and InbredSet.Name != 'BXD300' and
+                       and InbredSet.SpeciesId = Species.Id and
                        (PublishFreeze.InbredSetId = InbredSet.Id
                         or GenoFreeze.InbredSetId = InbredSet.Id
                         or ProbeFreeze.InbredSetId = InbredSet.Id)
                         group by InbredSet.Name
                         order by InbredSet.Name""" % species_name)
-        groups[species_name] = list(Cursor.fetchall())
+        results = Cursor.fetchall()
+        groups[species_name] = list(results)
     return groups
 
 
diff --git a/wqflask/wqflask/marker_regression/marker_regression.py b/wqflask/wqflask/marker_regression/marker_regression.py
index 9e01be3e..bcb14451 100644
--- a/wqflask/wqflask/marker_regression/marker_regression.py
+++ b/wqflask/wqflask/marker_regression/marker_regression.py
@@ -277,7 +277,7 @@ class MarkerRegression(object):
                     if ('lod_score' in marker.keys()) or ('lrs_value' in marker.keys()):
                         self.qtl_results.append(marker)
 
-            export_mapping_results(self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
+            export_mapping_results(self.dataset, self.this_trait, self.qtl_results, self.mapping_results_path, self.mapping_scale, self.score_type)
 
             self.trimmed_markers = trim_markers_for_table(results)
 
@@ -608,29 +608,35 @@ def create_snp_iterator_file(group):
     with gzip.open(snp_file_base, "wb") as fh:
         pickle.dump(data, fh, pickle.HIGHEST_PROTOCOL)
 
-def export_mapping_results(markers, results_path, mapping_scale, score_type):
+def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type):
     with open(results_path, "w+") as output_file:
-        output_file.write("Name\tChr\t")
+        output_file.write("Population: " + dataset.group.species.title() + " " + dataset.group.name + "\n")
+        output_file.write("Data Set: " + dataset.fullname + "\n")
+        if dataset.type == "ProbeSet":
+            output_file.write("Gene Symbol: " + trait.symbol + "\n")
+            output_file.write("Location: " + str(trait.chr) + " @ " + str(trait.mb) + " Mb\n")
+        output_file.write("\n")
+        output_file.write("Name,Chr,")
         if mapping_scale == "physic":
-            output_file.write("Mb\t" + score_type)
+            output_file.write("Mb," + score_type)
         else:
-            output_file.write("Cm\t" + score_type)
+            output_file.write("Cm," + score_type)
         if "additive" in markers[0].keys():
-            output_file.write("\tAdditive")
+            output_file.write(",Additive")
         if "dominance" in markers[0].keys():
-            output_file.write("\tDominance")
+            output_file.write(",Dominance")
         output_file.write("\n")
         for i, marker in enumerate(markers):
             logger.debug("THE MARKER:", marker)
-            output_file.write(marker['name'] + "\t" + str(marker['chr']) + "\t" + str(marker['Mb']) + "\t")
+            output_file.write(marker['name'] + "," + str(marker['chr']) + "," + str(marker['Mb']) + ",")
             if "lod_score" in marker.keys():
                 output_file.write(str(marker['lod_score']))
             else:
                 output_file.write(str(marker['lrs_value']))
             if "additive" in marker.keys():
-                output_file.write("\t" + str(marker['additive']))
+                output_file.write("," + str(marker['additive']))
             if "dominance" in marker.keys():
-                output_file.write("\t" + str(marker['dominance']))
+                output_file.write("," + str(marker['dominance']))
             if i < (len(markers) - 1):
                 output_file.write("\n")
 
diff --git a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
index 75767f47..8bdd91db 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
+++ b/wqflask/wqflask/static/new/javascript/dataset_menu_structure.json
@@ -2021,6 +2021,21 @@
                   "UCHSC BXD Whole Brain M430 2.0 (Nov06) RMA"
                ],
                [
+                  "113",
+                  "IBR_M_0606_R",
+                  "INIA Brain mRNA M430 (Jun06) RMA"
+               ],
+               [
+                  "101",
+                  "IBR_M_0106_P",
+                  "INIA Brain mRNA M430 (Jan06) PDNN"
+               ],
+               [
+                  "102",
+                  "IBR_M_0106_R",
+                  "INIA Brain mRNA M430 (Jan06) RMA"
+               ],
+               [
                   "95",
                   "BR_U_1105_P",
                   "UTHSC Brain mRNA U74Av2 (Nov05) PDNN"
@@ -2065,6 +2080,36 @@
             ],
             "Cerebellum mRNA": [
                [
+                  "72",
+                  "GCB_M2_0505_R",
+                  "GE-NIAAA Cerebellum mRNA M430v2 (May05) RMA"
+               ],
+               [
+                  "73",
+                  "GCB_M2_0505_P",
+                  "GE-NIAAA Cerebellum mRNA M430v2 (May05) PDNN"
+               ],
+               [
+                  "71",
+                  "GCB_M2_0505_M",
+                  "GE-NIAAA Cerebellum mRNA M430v2 (May05) MAS5"
+               ],
+               [
+                  "56",
+                  "CB_M_0305_R",
+                  "SJUT Cerebellum mRNA M430 (Mar05) RMA"
+               ],
+               [
+                  "55",
+                  "CB_M_0305_P",
+                  "SJUT Cerebellum mRNA M430 (Mar05) PDNN"
+               ],
+               [
+                  "54",
+                  "CB_M_0305_M",
+                  "SJUT Cerebellum mRNA M430 (Mar05) MAS5"
+               ],
+               [
                   "46",
                   "CB_M_1004_R",
                   "SJUT Cerebellum mRNA M430 (Oct04) RMA"
@@ -2909,6 +2954,39 @@
                ]
             ]
          },
+         "BXD300": {
+            "Genotypes": [
+               [
+                  "None",
+                  "BXD300Geno",
+                  "BXD300 Genotypes"
+               ]
+            ],
+            "Liver mRNA": [
+               [
+                  "105",
+                  "LV_G_0106_B",
+                  "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Both Sexes"
+               ],
+               [
+                  "103",
+                  "LV_G_0106_M",
+                  "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Males"
+               ],
+               [
+                  "104",
+                  "LV_G_0106_F",
+                  "UNC Agilent G4121A Liver LOWESS Stanford (Jan06) Females"
+               ]
+            ],
+            "Phenotypes": [
+               [
+                  "None",
+                  "BXD300Publish",
+                  "BXD300 Published Phenotypes"
+               ]
+            ]
+         },
          "BXH": {
             "Bone Femur mRNA": [
                [
@@ -3766,6 +3844,10 @@
             "BXD Bone"
          ],
          [
+            "BXD300",
+            "BXD300"
+         ],
+         [
             "BXH",
             "BXH"
          ],
@@ -4905,6 +4987,20 @@
                "Phenotypes"
             ]
          ],
+         "BXD300": [
+            [
+               "Phenotypes",
+               "Phenotypes"
+            ],
+            [
+               "Genotypes",
+               "Genotypes"
+            ],
+            [
+               "Liver mRNA",
+               "Liver mRNA"
+            ]
+         ],
          "BXH": [
             [
                "Phenotypes",
diff --git a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
index fd96eb78..d5ce6f84 100644
--- a/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
+++ b/wqflask/wqflask/static/new/javascript/dataset_select_menu_orig.js
@@ -24,6 +24,11 @@ $(function() {
     console.log("in populate group");
     species = $('#species').val();
     group_list = this.jdata.groups[species];
+    for (_i = 0, _len = group_list.length; _i < (_len - 1); _i++) {
+       if (group_list[_i][0] == "BXD300"){
+           group_list.splice(_i, 1)
+       }
+    }
     redo_dropdown($('#group'), group_list);
     if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option)
       return populate_type();
diff --git a/wqflask/wqflask/static/new/javascript/network_graph.js b/wqflask/wqflask/static/new/javascript/network_graph.js
index 0129bcae..0ecf4743 100644
--- a/wqflask/wqflask/static/new/javascript/network_graph.js
+++ b/wqflask/wqflask/static/new/javascript/network_graph.js
@@ -82,7 +82,7 @@ window.onload=function() {
         cy.nodes().qtip({
                             content: function(){
                                 qtip_content = ''
-                                gn_link = '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().id + '&dataset=' + this.data().dataset + '" >'+this.data().id +'</a>'+'</b><br>'
+                                gn_link = '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().id.split(":")[0] + '&dataset=' + this.data().id.split(":")[1] + '" >'+this.data().id +'</a>'+'</b><br>'
                                 qtip_content += gn_link
                                 if (typeof(this.data().geneid) !== 'undefined'){
                                     ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>'
@@ -92,15 +92,8 @@ window.onload=function() {
                                     omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>'
                                     qtip_content += omim_link
                                 }
-                                //qtip_content = gn_link + ncbi_link + omim_link
                                 return qtip_content
-                                //return '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.data().id + '&dataset=' + this.data().dataset + '" >'+this.data().id +'<a>'+'</b>' 
                             },
-                            // content: {
-                                // title: '<b>'+'<a href="http://gn2.genenetwork.org/show_trait?trait_id=' + this.target() + '&dataset=' + this.dataset() + '" >'+this.target() +'<a>'+'</b>',
-                                // text: this.target,
-                                // button: true
-                            // },
                             position: {
                                 my: 'top center',
                                 at: 'bottom center'
@@ -119,7 +112,7 @@ window.onload=function() {
                                 correlation_line = '<b>Sample r: ' + this.data().correlation + '</b><br>'
                                 p_value_line = 'Sample p(r): ' + this.data().p_value + '<br>'
                                 overlap_line = 'Overlap: ' + this.data().overlap + '<br>'
-                                scatter_plot = '<a href="http://gn2-zach.genenetwork.org/corr_scatter_plot?dataset_1=' + this.data().source_dataset + '&dataset_2=' + this.data().target_dataset + '&trait_1=' + this.data().source + '&trait_2=' + this.data().target + '" >View Scatterplot</a>'
+                                scatter_plot = '<a href="http://gn2-zach.genenetwork.org/corr_scatter_plot?dataset_1=' + this.data().source.split(":")[1] + '&dataset_2=' + this.data().target.split(":")[1] + '&trait_1=' + this.data().source.split(":")[0] + '&trait_2=' + this.data().target.split(":")[0] + '" >View Scatterplot</a>'
                                 return correlation_line + p_value_line + overlap_line + scatter_plot
                             },
                             position: {