Changeset 5730

Timestamp:

Nov 18, 2019, 2:12:54 PM (3 years ago)

Author:

Nicklas Nordborg

Message:

References #1199: Implement Variant calling pipeline

Added a dialog for displaying some information about the discovered variants. So far, the Gene name and an optional link to Cosmic is extracted and displayed. There is a lot more information and upon request it would be possible to display more.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/analysis/vcall_confirm.js (modified) (3 diffs)
• resources/analysis/view_variants.js (added)
• resources/analysis/view_variants.jsp (added)
• src/net/sf/basedb/reggie/JsonUtil.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/VariantCallingServlet.java (modified) (5 diffs)
• src/net/sf/basedb/reggie/vcf/VariantCallingInfoFactory.java (added)

extensions/net.sf.basedb.reggie/trunk/resources/analysis/vcall_confirm.js

@@ -97 +97 @@
       html += '<td>'+Reggie.formatCount(raw.VariantsRaw)+'</td>';
       html += '<td>';
-      html += raw.vcfFile ? raw.spots : '-';
+      if (raw.vcfFile)
+      {
+        html += raw.spots + '<span class="link vcf-link" data-file-id="'+raw.vcfFile.id+'" data-item-id="'+raw.id+'" title="View summary for the variants"><img src="../images/vcf_file.png" style="margin-left: 2px;"></span>';
+      }
       html += '</td>';
 
@@ -149 +152 @@
     }
 
+    var linkedVcf = document.getElementsByClassName('vcf-link');
+    for (var i = 0; i < linkedVcf.length; i++)
+    {
+      Events.addEventHandler(linkedVcf[i], 'click', vcall.vcfLinkOnClick);
+    }
+
+    
     Doc.show('step-1');
     Doc.show('goregister');
@@ -166 +176 @@
   }
   
-  
+  vcall.vcfLinkOnClick = function(event)
+  {
+    var fileId = Data.int(event.currentTarget, 'file-id');
+    var itemId = Data.int(event.currentTarget, 'item-id');
+    var url = 'view_variants.jsp?ID=' + App.getSessionId();
+    url += '&fileId='+fileId;
+    url += '&itemId='+itemId;
+    Dialogs.openPopup(url, 'ViewVcf', 900, 600);
+  }
+
   vcall.submit = function()
   {

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/JsonUtil.java

@@ -16 +16 @@
 import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DbControl;
+import net.sf.basedb.core.File;
 import net.sf.basedb.core.Hardware;
 import net.sf.basedb.core.Item;
@@ -260 +261 @@
     return json;
   }
+  
+  /**
+    @since 4.24
+  */
+  public static JSONObject getFileAsJSON(File file)
+  {
+    JSONObject jsonFile = new JSONObject();
+    jsonFile.put("id", file.getId());
+    jsonFile.put("name", file.getName());
+    jsonFile.put("size", file.getSize());
+    jsonFile.put("path", file.getPath().toString());
+    return jsonFile;
+  }
 
 }

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/VariantCallingServlet.java

@@ -2 +2 @@
 
 import java.io.IOException;
+import java.io.InputStream;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
+import java.util.zip.GZIPInputStream;
 
 import javax.servlet.ServletException;
@@ -52 +55 @@
 import net.sf.basedb.reggie.grid.ScriptUtil;
 import net.sf.basedb.reggie.grid.VariantCallingJobCreator;
+import net.sf.basedb.reggie.vcf.SnpData;
+import net.sf.basedb.reggie.vcf.VariantCallingInfoFactory;
+import net.sf.basedb.reggie.vcf.VcfParser;
+import net.sf.basedb.util.FileUtil;
 import net.sf.basedb.util.Values;
 import net.sf.basedb.util.error.ThrowableUtil;
@@ -169 +176 @@
           
           File vcf = raw.getFile(dc, Datafiletype.VCF);
-          if (vcf != null) raw.setAnnotation("vcfFile", vcf.getPath().toString());
+          if (vcf != null) raw.setAnnotation("vcfFile", JsonUtil.getFileAsJSON(vcf));
           
           // Load job information
@@ -187 +194 @@
         
         json.put("rawBioAssays", jsonRawBioAssays);
+      }
+      else if ("GetVcfStatistics".equals(cmd))
+      {
+        int fileId = Values.getInt(req.getParameter("fileId"));
+        int itemId = Values.getInt(req.getParameter("itemId"));
+        dc = sc.newDbControl();
+        
+        Rawbioassay vcall = Rawbioassay.getById(dc, itemId);
+        AlignedSequences alignment = vcall.getAlignedSequences(dc);
+        
+        vcall.setAnnotation("VariantsRaw", Annotationtype.VARIANTS_RAW.getAnnotationValue(dc, alignment.getItem()));
+
+        File vcf = File.getById(dc, fileId);
+        InputStream vcfIn = null;
+        try
+        {
+          VcfParser parser = new VcfParser();
+          parser.setUseLineNoAsId(true);
+          parser.setInfoFactory(new VariantCallingInfoFactory(
+              Arrays.asList("CCv87_ID"),
+              Arrays.asList("Gene_Name")
+              ));
+          vcfIn = vcf.getDownloadStream(0);
+          if (vcf.getName().endsWith(".gz")) vcfIn = new GZIPInputStream(vcfIn);
+          parser.parse(vcfIn, vcf.getName());
+          FileUtil.close(vcfIn);
+          
+          List<SnpData> snpList = parser.getSnpData();
+          JSONArray jsonSnp = new JSONArray();
+          for (SnpData snp : snpList)
+          {
+            jsonSnp.add(snp.asJSONObject());
+          }
+          
+          json.put("rawbioassay", vcall.asJSONObject());
+          json.put("snpData", jsonSnp);
+        }
+        finally
+        {
+          FileUtil.close(vcfIn);
+        }
       }
     
@@ -453 +501 @@
   
   
-
 }