Website Update

1. Add 2nd backup infos
2. Now in the download CSV files, the IDs and Names for genes and transcripts are separated (for both search page and evidence page)
3. Add buttons for linking to ShinyGO and GENEONTOLOGY

static/my.js

@@ -319,7 +319,13 @@ $(document).ready(function() {
           {
               className: "dt-head-center",
               targets: [0,1,2,3,4,5,6,7,8,9]
-          }
+          },
+          // hidden columns for downloading
+          {
+              targets: [10,11,12,13],
+              visible: false,
+              searchable: false
+          },
         ],
         dom:  "<'row'<'col-md-3'i><'col-md-5'p><'col-md-3'f><'col-md-1'B>>" +
           "<'row'<'col-md-12'tr>>",
@@ -329,10 +335,12 @@ $(document).ready(function() {
               text: 'Export',
               exportOptions: { // keep newline
                   stripNewlines: false,
-                  trim: false
+                  trim: false,
+                  columns: [0,10,11,12,13,3,4,5,6,7,8,9]
               }   
           }
-        ]
+        ],
+        processing: true
     } );
 } );
 
@@ -347,7 +355,13 @@ $(document).ready(function() {
           {
               className: "dt-head-center",
               targets: [0,1,2,3,4,5,6]
-          }
+          },
+          // hidden columns for downloading
+          {
+              targets: [7,8,9,10],
+              visible: false,
+              searchable: false
+          },
         ],
         dom:  "<'row'<'col-md-3'i><'col-md-5'p><'col-md-3'f><'col-md-1'B>>" +
           "<'row'<'col-md-12'tr>>",
@@ -357,7 +371,8 @@ $(document).ready(function() {
               text: 'Export',
               exportOptions: { // keep newline
                   stripNewlines: false,
-                  trim: false
+                  trim: false,
+                  columns: [0,1,7,8,9,10,4,5,6]
               }   
           }
         ]
@@ -418,7 +433,8 @@ $('#pathway').click(function () {
     // sorting will change the order of rows you get, but it does not matter
 
     // 3rd column: gene with href link, need parse
-    var gene = table.column(2).data()
+    // update: hidden column 12 gene ID; 13 gene symbol
+    var gene = table.column(12).data()
     // 5th column: free energy
     var mfe = table.column(4).data()
     // 7th column: matching length
@@ -428,14 +444,14 @@ $('#pathway').click(function () {
 
     // extract ensembl ID from links
     var len = gene.length
-    var pattern = />([a-zA-Z0-9_.]*?)<br/
+    // var pattern = />([a-zA-Z0-9_.]*?)<br/
     var obj = []
     for (var i = 0; i < len; i++) {
         // the first element will include the '>' and '<br'
         // ensemble ID is the 2nd element
         // only predictions from needed tool are included
         if (tool[i] == cur_tool) {
-            obj.push({ 'id': gene[i].match(pattern)[1], 'mfe': parseFloat(mfe[i]), 'mcl': parseInt(mcl[i]) })
+            obj.push({ 'id': gene[i], 'mfe': parseFloat(mfe[i]), 'mcl': parseInt(mcl[i]) })
         }
     }
 
@@ -465,4 +481,144 @@ $('#pathway').click(function () {
 
     // open a new window
     window.open('https://david.ncifcrf.gov/tools.jsp')    
-} )
+} )
+
+
+// onclick function to do GO analysis by ShinyGO
+// do not be affected by table filtering, that is, all entries will be included for ranking
+// only change the re-directing website
+$('#ShinyGO').click(function () {
+    // number of genes for pathway analysis
+    var num = document.getElementById('mrna_num').value
+
+    // prediction tool
+    var cur_tool = $('input[name=search_table]:checked').val()
+    if (cur_tool == 'Consensus') {cur_tool='IntaRNA'}
+
+    // get values from datatable
+    var table = $('#table_id').DataTable()
+
+    // get column value, index start from 0
+    // you can get all rows no matter whether filter is activated
+    // sorting will change the order of rows you get, but it does not matter
+
+    // 3rd column: gene with href link, need parse
+    // update: hidden column 12 gene ID; 13 gene symbol
+    var gene = table.column(12).data()
+    // 5th column: free energy
+    var mfe = table.column(4).data()
+    // 7th column: matching length
+    var mcl = table.column(6).data()
+    // 4th column: prediction tool
+    var tool = table.column(3).data()
+
+    // extract ensembl ID from links
+    var len = gene.length
+    // var pattern = />([a-zA-Z0-9_.]*?)<br/
+    var obj = []
+    for (var i = 0; i < len; i++) {
+        // the first element will include the '>' and '<br'
+        // ensemble ID is the 2nd element
+        // only predictions from needed tool are included
+        if (tool[i] == cur_tool) {
+            obj.push({ 'id': gene[i], 'mfe': parseFloat(mfe[i]), 'mcl': parseInt(mcl[i]) })
+        }
+    }
+
+
+    // sort gene ids based mfe and mcl
+    // +/- to indicate ascending or descending order
+    // sort genes with lowest mfe first
+    // with ties going to the genes with the highest mcl
+    // sorting result checked, it's corrected
+    obj.sort(getSortMethod('+mfe', '-mcl'))
+
+    // get needed sorted gene ids
+    if (num > obj.length) {
+        num = obj.length
+    }
+
+    var sorted_ids = []
+    for (var i = 0; i < num; i++) {
+        sorted_ids[i] = obj[i].id
+    }
+
+    // copy procedure checked, list is completed, and the order is corrected
+    copyToClipboard(sorted_ids)
+
+    // David can also support both human and mouse 
+    alert('A list of top ' + num + ' Gene Ensemble IDs copied to clipboard. Paste them into the input box in ShinyGO website and start GO Enrichment Analysis')
+
+    // open a new window
+    window.open('http://bioinformatics.sdstate.edu/go/')    
+} )
+
+
+// onclick function to do GO analysis by GENE ONTOLOGY
+// do not be affected by table filtering, that is, all entries will be included for ranking
+// change the re-directing website; use gene symbols instead of IDs; use /n instead of , to separate genes
+$('#GENEONTOLOGY').click(function () {
+    // number of genes for pathway analysis
+    var num = document.getElementById('mrna_num').value
+
+    // prediction tool
+    var cur_tool = $('input[name=search_table]:checked').val()
+    if (cur_tool == 'Consensus') {cur_tool='IntaRNA'}
+
+    // get values from datatable
+    var table = $('#table_id').DataTable()
+
+    // get column value, index start from 0
+    // you can get all rows no matter whether filter is activated
+    // sorting will change the order of rows you get, but it does not matter
+
+    // 3rd column: gene with href link, need parse
+    // update: hidden column 12 gene ID; 13 gene symbol
+    var gene = table.column(13).data()
+    // 5th column: free energy
+    var mfe = table.column(4).data()
+    // 7th column: matching length
+    var mcl = table.column(6).data()
+    // 4th column: prediction tool
+    var tool = table.column(3).data()
+
+    // extract ensembl ID from links
+    var len = gene.length
+    // var pattern = />([a-zA-Z0-9_.]*?)<br/
+    var obj = []
+    for (var i = 0; i < len; i++) {
+        // the first element will include the '>' and '<br'
+        // ensemble ID is the 2nd element
+        // only predictions from needed tool are included
+        if (tool[i] == cur_tool) {
+            obj.push({ 'id': gene[i], 'mfe': parseFloat(mfe[i]), 'mcl': parseInt(mcl[i]) })
+        }
+    }
+
+
+    // sort gene ids based mfe and mcl
+    // +/- to indicate ascending or descending order
+    // sort genes with lowest mfe first
+    // with ties going to the genes with the highest mcl
+    // sorting result checked, it's corrected
+    obj.sort(getSortMethod('+mfe', '-mcl'))
+
+    // get needed sorted gene ids
+    if (num > obj.length) {
+        num = obj.length
+    }
+
+    var sorted_ids = []
+    for (var i = 0; i < num; i++) {
+        sorted_ids[i] = obj[i].id
+    }
+
+    // copy procedure checked, list is completed, and the order is corrected
+    copyToClipboard(sorted_ids.join("\r\n"))
+
+    // David can also support both human and mouse 
+    alert('A list of top ' + num + ' Gene Symbols copied to clipboard. Paste them into the input box in GENE ONTOLOGY website and start GO Enrichment Analysis')
+
+    // open a new window
+    window.open('http://geneontology.org/')    
+} )