updated format for variants

frontend-js/package.json

@@ -37,7 +37,7 @@
     "mkdirp": "^0.5.1",
     "mocha": "^3.5.3",
     "mock-local-storage": "^1.1.8",
-    "molart": "1.3.1",
+    "molart": "1.3.2",
     "stream-to-blob": "^1.0.1",
     "uglifyjs": "^2.4.10"
   },

frontend-js/src/main/js/map/structure/MolArt.js

@@ -157,7 +157,7 @@ MolArt.prototype._activate = function (uniprotId) {
         var customDataSources = [];
         for (var i = 0; i < variants.length; i++) {
           customDataSources.push({
-            source: 'MINERVA overlay <br/>' + variants[i].overlayName,
+            source: 'MINERVA: ' + variants[i].overlayName,
             useExtension: false,
             data: constructVariantsData(sequence, variants[i].variants)
           });
@@ -251,15 +251,19 @@ var processGeneVariant = function(minervaVariant) {
   // nonsynonymous_SNV	TRIB3:NM_001301188:exon2:c.G82A:p.E28K,TRIB3:NM_001301190:exon2:c.G82A:p.E28K,TRIB3:NM_001301193:exon2:c.G82A:p.E28K,TRIB3:NM_001301196:exon2:c.G82A:p.E28K,TRIB3:NM_021158:exon2:c.G82A:p.E28K,TRIB3:NM_001301201:exon3:c.G163A:p.E55K
 
   // frameshift insertion: LRRK2:NM_198578:exon1:c.151_152insCCTCCAAGTTATTTCAAGGCAAAAATATCCATGTGCCTCT:p.A51fs
+  // frameshift insertion: p.A51fsins
   // frameshift insertion: NCOA3:NM_001174087:exon22:c.4171_4172insG:p.M1391fs,NCOA3:NM_001174088:exon22:c.4147_4148insG:p.M1383fs,NCOA3:NM_006534:exon22:c.4162_4163insG:p.M1388fs,NCOA3:NM_181659:exon22:c.4174_4175insG:p.M1392fs
   
   // nonframeshift_insertion	LRRK2:NM_198578:exon27:c.3777_3778insATTCCTCCT:p.E1259delinsEIPP
+  // nonframeshift_insertion	p.E1259delinsEIPP
   // nonframeshift_insertion SYNJ1:NM_001160306:exon28:c.3957_3958insAATACT:p.L1320delinsNTL,SYNJ1:NM_003895:exon32:c.4215_4216insAATACT:p.L1406delinsNTL
 
   // frameshift_deletion	LRRK2:NM_198578:exon17:c.2069_2070del:p.Q690fs
-  // frameshift_deletion ESF1:NM_001276380:exon14:c.2519_2520del:p.E840fs,ESF1:NM_016649:exon14:c.2519_2520del:p.E840fs
+  // frameshift_deletion	p.Q690fsdel
+  // frameshift_deletion ESF1:NM_001276380:exon14:c.2519_2520del:p.E840fs,ESF1:NM_016649:exon14:c.2519_2520del:p.E840fsins
 
   // nonframeshift_deletion	LRRK2:NM_198578:exon9:c.1099_1101del:p.367_367del
+  // nonframeshift_deletion	p.367_367del
   // nonframeshift_deletion	RRBP1:NM_004587:exon15:c.2022_2024del:p.674_675del,RRBP1:NM_001042576:exon16:c.2022_2024del:p.674_675del
   
   
@@ -270,35 +274,45 @@ var processGeneVariant = function(minervaVariant) {
 
   for (var i =0; i < sChange.length; i++) {
 
-    var aaChange = sChange[i].split('.').slice(-1)[0]; // LRRK2:NM_198578:exon1:c.T45C:p.T15T
-    var variant = new Variant();
+    try {
 
-    if (aaChange.endsWith('del') > 0) {      
-      
-      var m = aaChange.match( /(\d+)_(\d+)/ );
-      [, variant.posFrom, variant.posTo] = m;
-      variant.varType = 'Nonframeshift deletion'  
-      
-    } else if (aaChange.endsWith('fs') || aaChange.indexOf('delins') >=0) {
-      
-      var m = aaChange.match( /([A-Z])(\d+)/ );
-      [ ,variant.aaFrom, variant.posFrom] = m;      
-      if (change.indexOf('delins') >= 0 ) variant.varType = 'Nonframeshift insertion';
-      else if (change.indexOf('del') >= 0)   variant.varType = 'Frameshift deletion';
-      else variant.varType = 'Frameshift insertion';       
-      
-    } else {
+      var aaChange = sChange[i].split('.').slice(-1)[0]; // LRRK2:NM_198578:exon1:c.T45C:p.T15T
+      var variant = new Variant();
 
-      var m = aaChange.match( /([a-zA-Z]+)(\d+)([a-zA-Z])+/ );
-      
-      if (!m || m.length != 4) continue;
+      if (aaChange.endsWith('del') > 0) {      
+        
+        var m = aaChange.match( /(\d+)_(\d+)/ );
+        [, variant.posFrom, variant.posTo] = m;
+        variant.varType = 'Nonframeshift deletion'  
+        
+      }else if (aaChange.indexOf('delins') >=0) {
+        var m = aaChange.match( /([A-Z])(\d+)delins([A-Z]+)/ );
+        [ ,variant.aaFrom, variant.posFrom, variant.aaTo] = m;      
+        variant.aaTo = 'delins: ' + variant.aaTo; //This is because ProtVista can't handle insertions so we need to prefix it by 'd' which will place the variant into the 'd' line
+        variant.varType = 'Nonframeshift insertion';      
+      }
+      else if (aaChange.endsWith('fs')) {
+        
+        var m = aaChange.match( /([A-Z])(\d+)/ );
+        [ ,variant.aaFrom, variant.posFrom] = m;            
+        if (change.indexOf('del') >= 0)   variant.varType = 'Frameshift deletion';
+        else variant.varType = 'Frameshift insertion';       
+        
+      } else {
 
-      [ ,variant.aaFrom, variant.posFrom, variant.aaTo] = m;      
-      variant.varType = variant.aaFrom == variant.aaTo ? 'Synonymous SNV' : 'Nonsynonymous SNV';      
+        var m = aaChange.match( /([a-zA-Z]+)(\d+)([a-zA-Z])+/ );
+        
+        if (!m || m.length != 4) continue;
 
+        [ ,variant.aaFrom, variant.posFrom, variant.aaTo] = m;      
+        variant.varType = variant.aaFrom == variant.aaTo ? 'Synonymous SNV' : 'Nonsynonymous SNV';      
+
+      }
+      
+      vars.push(variant);
+    } catch (err) {
+      console.error("Problem with parsing variant " + minervaVariant.getAminoAcidChange(), err);
     }
-    
-    vars.push(variant);
   }  
   
   return vars;