Changeset 5805


Ignore:
Timestamp:
Jan 9, 2020, 9:49:48 AM (2 years ago)
Author:
Nicklas Nordborg
Message:

References #1221: Display more information in the Variant summary dialog

Added TYPE and dbSNP fields and changed the Gene field to use ncbiRefSeq instead of ANN.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
3 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/resources/analysis/view_variants.js

    r5735 r5805  
    2828      var info = snp.info;
    2929      var cosmicId = info['cosmic_ID'];
     30      var dbSnpId = info['dbsnp_ID'];
    3031      html += '<tr class="snp highlight">';
    3132      html += '<td>'+Strings.encodeTags(snp.chromosome+':'+snp.position)+'</td>';
    3233      html += '<td class="dottedleft ref">'+Strings.encodeTags(snp.ref+' › '+snp.alt)+'</td>';
    33       html += '<td class="dottedleft">'+vgt.getAnnValues(info, 'Gene_Name')+'</td>';
     34      html += '<td class="dottedleft">'+Strings.encodeTags(info['TYPE'])+'</td>';
     35      html += '<td class="dottedleft">'+Strings.encodeTags(info['ncbiRefSeq'])+'</td>';
    3436      html += '<td class="dottedleft">'+vgt.getCosmicLink(cosmicId)+'</td>';
     37      html += '<td class="dottedleft">'+vgt.getDbSnpLink(dbSnpId)+'</td>';
    3538      html += '</tr>';
    3639    }
     
    7073  }
    7174 
     75  vgt.getDbSnpLink = function(rsId)
     76  {
     77    if (!rsId) return '';
     78
     79    var tmp = rsId.split(',');
     80    var links = [];
     81    for (var i = 0; i < tmp.length; i++)
     82    {
     83      var link = '<a target="_blank" title="View in dbSNP (new window)"';
     84      link += ' href="https://www.ncbi.nlm.nih.gov/snp/'+encodeURIComponent(tmp[i])+'">';
     85      link += Strings.encodeTags(tmp[i])+'</a>';
     86     
     87      links[i] = link;
     88    }
     89    return links.join(', ');
     90  }
     91 
    7292  return vgt;
    7393}();
  • extensions/net.sf.basedb.reggie/trunk/resources/analysis/view_variants.jsp

    r5730 r5805  
    9494      <th>Location</th>
    9595      <th class="dottedleft ref">Ref › Alt</th>
     96      <th class="dottedleft">Type</th>
    9697      <th class="dottedleft">Gene</th>
    9798      <th class="dottedleft">Cosmic ID</th>
     99      <th class="dottedleft">dbSNP ID</th>
    98100    </tr>
    99101    <tbody id="snp-list"></tbody>
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/VariantCallingServlet.java

    r5776 r5805  
    217217          parser.setUseLineNoAsId(true);
    218218          parser.setInfoFactory(new VariantCallingInfoFactory(
    219               Arrays.asList("cosmic_ID"),
    220               Arrays.asList("Gene_Name")
     219              Arrays.asList("TYPE", "ncbiRefSeq", "cosmic_ID", "dbsnp_ID"),
     220              null
    221221              ));
    222222          vcfIn = vcf.getDownloadStream(0);
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