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August 4, 2010 19:46
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| <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> | |
| <html | |
| xmlns='http://www.w3.org/1999/xhtml' | |
| xmlns:svg="http://www.w3.org/2000/svg" | |
| xmlns:xlink="http://www.w3.org/1999/xlink" | |
| > | |
| <!-- | |
| Author: | |
| Pierre Lindenbaum PhD. 2010 | |
| [email protected] | |
| http://plindenbaum.blogspot.com | |
| Motivation: | |
| small embedded genome browser | |
| --> | |
| <head> | |
| <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"/> | |
| <style type='text/css'> | |
| body { | |
| color:rgb(50,50,50); | |
| margin:20px; | |
| padding:20px; | |
| font: 12pt Arial, Helvetica, sans-serif; | |
| } | |
| th { | |
| font-size:150%; | |
| text-align:center; | |
| color:skyblue; | |
| background-color:teal; | |
| } | |
| label { | |
| text-align:right; | |
| } | |
| button { | |
| border: 1px solid; | |
| background-image:-moz-linear-gradient( top, gray, lightgray ); | |
| } | |
| button:hover { | |
| background-image:-moz-linear-gradient( top, lightgray, gray ); | |
| } | |
| </style> | |
| <script type="text/javascript" src="genes.json"/> | |
| <script type="text/javascript" src="variations.json"/> | |
| <script type="text/javascript"> | |
| var SVG="http://www.w3.org/2000/svg"; | |
| var XHTML="http://www.w3.org/1999/xhtml"; | |
| var XLINK="http://www.w3.org/1999/xlink"; | |
| /** feature Height */ | |
| var featureHeight=12; | |
| /** space between features */ | |
| var featureSpacing=2; | |
| /** view pixel */ | |
| var paneWidth=700; | |
| /** left Margin */ | |
| var leftMargin=100; | |
| /** top Margin */ | |
| var topMargin=30; | |
| /** chromosome start */ | |
| var chromStart=350000000; | |
| /** chromosome end */ | |
| var chromEnd=0; | |
| /** view start */ | |
| var viewStart=0; | |
| /** view end */ | |
| var viewLength=0; | |
| function niceNumber(val) | |
| { | |
| var s=""+(val); | |
| var s2=""; | |
| if(s.length<=3) return s; | |
| while(s.length > 3) | |
| { | |
| s2=s.substring(s.length-3,s.length)+(s2.length==0?"":","+s2); | |
| s=s.substring(0,s.length-3); | |
| } | |
| s2=s+","+s2; | |
| return s2; | |
| } | |
| function removeChildren(node) | |
| { | |
| while(node.hasChildNodes()) | |
| { | |
| node.removeChild(node.firstChild); | |
| } | |
| return node; | |
| } | |
| function makeLink(url) | |
| { | |
| var a=document.createElementNS(SVG,"a"); | |
| a.setAttributeNS(XLINK,"xlink:href",url); | |
| return a; | |
| } | |
| function makeText(x,y,text) | |
| { | |
| var t=document.createElementNS(SVG,"text"); | |
| t.setAttribute("x",x); | |
| t.setAttribute("y",y); | |
| t.appendChild(document.createTextNode(text)); | |
| return t; | |
| } | |
| function makeRect(x,y,width,height) | |
| { | |
| var rect=document.createElementNS(SVG,"rect"); | |
| rect.setAttribute("x",x); | |
| rect.setAttribute("y",y); | |
| rect.setAttribute("width",width); | |
| rect.setAttribute("height",height); | |
| return rect; | |
| } | |
| function makeRect2(x1,y,x2,height) | |
| { | |
| return makeRect(x1,y,x2-x1,height); | |
| } | |
| function makeLine(x1,y1,x2,y2) | |
| { | |
| var L=document.createElementNS(SVG,"line"); | |
| L.setAttribute("x1",x1); | |
| L.setAttribute("y1",y1); | |
| L.setAttribute("x2",x2); | |
| L.setAttribute("y2",y2); | |
| return L; | |
| } | |
| function pos2pixel(pos) | |
| { | |
| return ((pos-viewStart)/(viewLength*1.0))*(paneWidth); | |
| } | |
| function pos2trim(pos) | |
| { | |
| var pix=pos2pixel(pos); | |
| if(pix<0) pix=0; | |
| if(pix>paneWidth) pix=paneWidth; | |
| return pix; | |
| } | |
| function makeKnownGene(kg) | |
| { | |
| var g=document.createElementNS(SVG,"g"); | |
| g.setAttribute("title",kg.name); | |
| if(!( pos2trim(kg.cdsStart)==pos2trim(kg.txStart) && | |
| pos2trim(kg.cdsEnd)==pos2trim(kg.txEnd))) | |
| { | |
| /* transcription */ | |
| var tx=makeLine(pos2trim(kg.txStart),0,pos2trim(kg.txEnd),0); | |
| tx.setAttribute("style","stroke:black;"); | |
| g.appendChild(tx); | |
| } | |
| /** CDS */ | |
| var cds=makeRect2(pos2trim(kg.cdsStart),-2,pos2trim(kg.cdsEnd),4); | |
| cds.setAttribute("style","stroke:black;fill:url(#grad2);"); | |
| g.appendChild(cds); | |
| var h2=Math.round((featureHeight-2)/2); | |
| var prev=-1; | |
| for(var exonIndex=0; exonIndex < kg.exonCount; exonIndex++) | |
| { | |
| if(kg.exonEnds[exonIndex] < viewStart) continue; | |
| if(kg.exonStarts[exonIndex] > (viewStart+viewLength) ) continue; | |
| var exonStart = pos2trim(kg.exonStarts[exonIndex]); | |
| var exonEnd = pos2trim(kg.exonEnds[exonIndex]); | |
| if(prev==Math.round(exonEnd)) continue; | |
| prev=Math.round(exonEnd); | |
| var exonElt = makeRect2(exonStart,-h2,exonEnd,h2*2); | |
| exonElt.setAttribute("style","stroke:black;fill:url(#grad1);"); | |
| g.appendChild(exonElt); | |
| } | |
| return g; | |
| } | |
| function focusKg(index) | |
| { | |
| var kg=knownGenes[index]; | |
| viewStart=kg.txStart; | |
| viewLength=kg.txEnd-viewStart; | |
| updateTitle(kg.name); | |
| reload(); | |
| } | |
| function updateTitle(prefix) | |
| { | |
| var title=removeChildren(document.getElementById('browserTitle')); | |
| title.appendChild(document.createTextNode( | |
| (prefix==null?"":prefix+" ")+ | |
| knownGenes[0].chrom+":"+niceNumber(viewStart+1)+"-"+niceNumber(viewStart+viewLength+1)+ | |
| " size:"+niceNumber(viewLength))); | |
| } | |
| function zoomOut(percent) | |
| { | |
| var mid=Math.round(viewStart+viewLength/2); | |
| var chromLength=chromEnd-chromStart; | |
| var newLength=Math.round(viewLength*percent); | |
| if(newLength > chromLength) newLength=chromLength; | |
| if(newLength < 1) newLength=1; | |
| viewLength=newLength; | |
| viewStart=Math.round(mid-viewLength/2); | |
| if(viewStart+viewLength >= chromEnd) viewStart=chromEnd-viewLength; | |
| if(viewStart <= chromStart) viewStart=chromStart; | |
| updateTitle(null); | |
| reload(); | |
| } | |
| function zoomIn(percent) | |
| { | |
| zoomOut(1.0/percent); | |
| } | |
| function moveView(side,percent) | |
| { | |
| //var chromLength=chromEnd-chromStart; | |
| var shift=Math.round(viewLength*percent); | |
| if(shift < 1) shift=1; | |
| if(side<0) | |
| { | |
| newStart=viewStart-shift; | |
| if(newStart< chromStart) newStart=chromStart; | |
| } | |
| else | |
| { | |
| newStart=viewStart+shift; | |
| if(newStart + viewLength > chromEnd) newStart=chromEnd-shift; | |
| } | |
| viewStart=newStart; | |
| updateTitle(null); | |
| reload(); | |
| } | |
| function searchTerm(term) | |
| { | |
| var newStart=-1; | |
| var newEnd=-1; | |
| var t2=term.replace(/[,]/g,""); | |
| if(term.length==0) return; | |
| if(t2.match(/^\d+$/)) | |
| { | |
| var n=parseInt(t2); | |
| if(n>= chromStart && n< chromEnd) | |
| { | |
| newStart=n-1; | |
| newEnd=n; | |
| } | |
| } | |
| else if(t2.match(/^\d+\-\d+$/)) | |
| { | |
| var x=t2.indexOf("-"); | |
| var n1=parseInt(t2.substr(0,x)); | |
| var n2=parseInt(t2.substr(x+1)); | |
| if(n1<=n2 && n1>= chromStart && n2< chromEnd) | |
| { | |
| newStart=n1-1; | |
| newEnd=n2-1; | |
| } | |
| } | |
| else | |
| { | |
| for(var i=0;i < knownGenes.length; ++i) | |
| { | |
| var kg=knownGenes[i]; | |
| if(kg.name==term || term==kg.proteinID) | |
| { | |
| newStart=kg.txStart; | |
| newEnd=kg.txEnd; | |
| break; | |
| } | |
| } | |
| } | |
| if(newStart!=-1) | |
| { | |
| viewStart=newStart; | |
| viewLength=(newEnd-newStart); | |
| updateTitle(null); | |
| reload(); | |
| } | |
| } | |
| function searchVar(orient) | |
| { | |
| var i; | |
| var index_snp=-1; | |
| if(orient==-1) | |
| { | |
| for(var i=0;i < variations.length; ++i) | |
| { | |
| var snp=variations[i]; | |
| if(snp.start >= viewStart ) break; | |
| if(!acceptVar(snp)) continue; | |
| index_snp=i; | |
| } | |
| } | |
| else | |
| { | |
| for(var i=0;i < variations.length; ++i) | |
| { | |
| var snp=variations[i]; | |
| if(snp.start <= (viewStart+viewLength) ) continue; | |
| if(!acceptVar(snp)) continue; | |
| index_snp=i; | |
| break; | |
| } | |
| } | |
| if(index_snp==-1) | |
| { | |
| alert("Not found."); | |
| return; | |
| } | |
| viewStart=Math.round(variations[index_snp].start-viewLength/2); | |
| if(viewStart+viewLength >= chromEnd) viewStart=chromEnd-viewLength; | |
| if(viewStart <= chromStart) viewStart=chromStart; | |
| updateTitle(null); | |
| reload(); | |
| } | |
| function acceptVar(snp) | |
| { | |
| var sel=document.getElementById('selsnp'); | |
| switch(sel.selectedIndex) | |
| { | |
| case 1: if(snp.rs==null) { return false;} break; | |
| case 2: if(snp.rs!=null) {return false;} break; | |
| default:break; | |
| } | |
| sel=document.getElementById('seltype'); | |
| switch(sel.selectedIndex) | |
| { | |
| //case 1: if(snp.struct) { return false;} break; | |
| //case 2: if(!snp.struct) { return false;} break; | |
| default:break; | |
| } | |
| sel=document.getElementById('selsift'); | |
| switch(sel.selectedIndex) | |
| { | |
| case 1: if(snp.sift!="DAMAGING") { return false;} break; | |
| case 2: if(snp.sift!="DAMAGING *Warning! Low confidence.") { return false;} break; | |
| case 3: if(snp.sift!="N/A") { return false;} break; | |
| case 4: if(snp.sift!="Not scored") { return false;} break; | |
| case 5: if(snp.sift!="TOLERATED") { return false;} break; | |
| default:break; | |
| } | |
| for(var p=0;p<2;p++) | |
| { | |
| sel=document.getElementById(p==0?'selpph2var':'selpph2div'); | |
| var pred=(p==0?snp.pph2var:snp.pph2div); | |
| switch(sel.selectedIndex) | |
| { | |
| case 1: if(pred!="benign") { return false;} break; | |
| case 2: if(pred!="possibly damaging") { return false;} break; | |
| case 3: if(pred!="probably damaging") { return false;} break; | |
| case 4: if(pred!="unknown") { return false;} break; | |
| default:break; | |
| } | |
| } | |
| var checkbox=document.getElementById('checkHQ'); | |
| if(checkbox.checked && snp.hq!=true) return false; | |
| return true; | |
| } | |
| function reload() | |
| { | |
| paneWidth= Math.round(window.innerWidth*0.8)-(leftMargin-1); | |
| if(paneWidth <= leftMargin+100) paneWidth=leftMargin+100; | |
| var svg=document.getElementById('main'); | |
| var svgContent=removeChildren(document.getElementById('mainG')); | |
| svg.setAttribute("width",(paneWidth+leftMargin+1)); | |
| var rect=makeRect(1,1,(paneWidth+leftMargin+1)-1,0); | |
| rect.setAttribute("style","fill:url(#grad0);stroke:black;"); | |
| svgContent.appendChild(rect); | |
| var y=topMargin; | |
| for(var i=0;i < knownGenes.length; ++i) | |
| { | |
| var kg=knownGenes[i]; | |
| if( viewStart >= kg.txEnd) continue; | |
| if( kg.txStart > (viewStart+viewLength) ) continue; | |
| var g=makeKnownGene(kg); | |
| g.setAttribute("transform","translate("+leftMargin+","+y+")"); | |
| var a= makeLink("javascript:focusKg("+i+");"); | |
| a.appendChild(g); | |
| svgContent.appendChild(a); | |
| var geneName=kg.name; | |
| if(kg.proteinID!=null &&kg.proteinID.length >0) | |
| { | |
| geneName=kg.proteinID; | |
| } | |
| var titleElt= makeText(0,0,geneName); | |
| titleElt.setAttribute("transform","translate("+(leftMargin-1)+","+(y+featureHeight/2)+")"); | |
| titleElt.setAttribute("style","text-anchor:end;");//alignment-baseline:middle; | |
| a=makeLink("http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg18&position="+kg.name); | |
| a.setAttribute("target","_blank"); | |
| a.appendChild(titleElt); | |
| svgContent.appendChild(a); | |
| y+=(featureSpacing+featureHeight); | |
| } | |
| var nVariationsInTable=0; | |
| var tBody=removeChildren(document.getElementById('Tbody')); | |
| for(var i=0;i < variations.length; ++i) | |
| { | |
| var snp=variations[i]; | |
| if(snp.end < viewStart) continue; | |
| if(snp.start > (viewLength+viewStart)) continue; | |
| if(!acceptVar(snp)) continue; | |
| if(nVariationsInTable<1000) | |
| { | |
| var tr=document.createElementNS(XHTML,"tr"); | |
| tr.setAttribute("style","background:"+(nVariationsInTable%2==0?"lavender":"whitesmoke")+";"); | |
| tBody.appendChild(tr); | |
| var td=document.createElementNS(XHTML,"td"); | |
| tr.appendChild(td); | |
| var a=document.createElementNS(XHTML,"a"); | |
| a.setAttribute("href","http://genome.ucsc.edu/cgi-bin/hgTracks?org=Human&db=hg18&position="+snp.chrom+":"+snp.start); | |
| a.setAttribute("target","_blank"); | |
| a.appendChild(document.createTextNode(snp.chrom+":"+niceNumber(snp.start)+"-"+niceNumber(snp.end))); | |
| td.appendChild(a); | |
| td=document.createElementNS(XHTML,"td"); | |
| tr.appendChild(td); | |
| if(!snp.struct) td.appendChild(document.createTextNode(snp.ref)); | |
| td=document.createElementNS(XHTML,"td"); | |
| tr.appendChild(td); | |
| if(!snp.struct) td.appendChild(document.createTextNode(snp.alt)); | |
| td=document.createElementNS(XHTML,"td"); | |
| tr.appendChild(td); | |
| td.appendChild(document.createTextNode(niceNumber(snp.depth))); | |
| td=document.createElementNS(XHTML,"td"); | |
| tr.appendChild(td); | |
| if(!snp.struct && snp.rs!=null) | |
| { | |
| a=document.createElementNS(XHTML,"a"); | |
| a.setAttribute("href","http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?rs="+snp.rs); | |
| a.setAttribute("target","_blank"); | |
| a.appendChild(document.createTextNode(snp.rs)); | |
| td.appendChild(a); | |
| } | |
| td=document.createElementNS(XHTML,"td"); | |
| tr.appendChild(td); | |
| if(snp.sift!=null) | |
| { | |
| td.appendChild(document.createTextNode(snp.sift)); | |
| } | |
| td=document.createElementNS(XHTML,"td"); | |
| tr.appendChild(td); | |
| if(snp.pph2var!=null) | |
| { | |
| td.appendChild(document.createTextNode(snp.pph2var)); | |
| } | |
| td=document.createElementNS(XHTML,"td"); | |
| tr.appendChild(td); | |
| if(snp.pph2div!=null) | |
| { | |
| td.appendChild(document.createTextNode(snp.pph2div)); | |
| } | |
| nVariationsInTable++; | |
| } | |
| var snpStart = pos2trim(snp.start); | |
| var snpEnd = pos2trim(snp.end); | |
| if(snpEnd==snpStart) snpEnd++; | |
| var L=makeRect2(snpStart,0,snpEnd,y); | |
| L.setAttribute("transform","translate("+leftMargin+",0)"); | |
| L.setAttribute("style","stroke:red;opacity:0.3;"); | |
| L.setAttribute("title","Variation "+snp.rs); | |
| svgContent.appendChild(L); | |
| } | |
| rect.setAttribute("height",y-1); | |
| svg.setAttribute("height",y); | |
| } | |
| function init() | |
| { | |
| var i; | |
| for(i=0;i < variations.length; ++i) | |
| { | |
| var snp=variations[i]; | |
| if(chromStart > snp.start) chromStart=snp.start; | |
| if(chromEnd < snp.end) chromEnd=snp.end; | |
| } | |
| chromStart-=10; | |
| chromEnd+=10; | |
| i=0; | |
| while(i < knownGenes.length) | |
| { | |
| var kg=knownGenes[i]; | |
| if(chromEnd < kg.txStart || chromStart > kg.txEnd) | |
| { | |
| knownGenes.splice(i,1); | |
| } | |
| else | |
| { | |
| kg.id=i; | |
| i++; | |
| } | |
| } | |
| viewStart=chromStart; | |
| viewLength=chromEnd-chromStart; | |
| if(knownGenes.length>0) focusKg(0); | |
| } | |
| </script> | |
| </head> | |
| <body onload="init();"> | |
| <div style="text-align:center;"> | |
| <div style="font-size:200%;margin:10px;" id="browserTitle">Title</div> | |
| <div><label>Move</label> | |
| <button onclick="moveView(-1,0.95);" title="move 95% left">⇚</button> | |
| <button onclick="moveView(-1,0.475);" title="move 47% left">⇐</button> | |
| <button onclick="moveView(-1,0.1);" title="move 10% left">←</button> | |
| <button onclick="moveView(1,0.1);" title="move 10% right">→</button> | |
| <button onclick="moveView(1,0.475);" title="move 47% right">⇒</button> | |
| <button onclick="moveView(1,0.95);" title="move 95% right">⇛</button> | |
| <label>Zoom In</label> | |
| <button onclick="zoomIn(1.5);" title="zoom in 1.5x">1.5x</button> | |
| <button onclick="zoomIn(3.0);" title="zoom in 3.0x">3x</button> | |
| <button onclick="zoomIn(10.0);" title="zoom in 10x">1Ox</button> | |
| <label>Zoom Out</label> | |
| <button onclick="zoomOut(1.5);" title="zoom out 1.5x">1.5x</button> | |
| <button onclick="zoomOut(3.0);" title="zoom out 3.0x">3x</button> | |
| <button onclick="zoomOut(10.0);" title="zoom out 10x">1Ox</button> | |
| <label>Search:</label> | |
| <button onclick="searchVar(-1);" title="find next variation on the left">←</button> | |
| <button onclick="searchVar(1);" title="find next variation on the right">→</button> | |
| <label for="term" title="position or start-end or gene name or gene proteinID">Find:</label> | |
| <input id="term" size="12" onchange="searchTerm(this.value);" title="position or start-end or gene name or gene proteinID"/> | |
| </div> | |
| <div> | |
| <label>SNP:</label> | |
| <select id="selsnp" onchange="reload();"> | |
| <option>All</option> | |
| <option>rs###</option> | |
| <option>new</option> | |
| </select> | |
| <span style="visibility:hidden"><label>Type:</label> | |
| <select id="seltype" onchange="reload();"> | |
| <option>All</option> | |
| <option selected="true">Diff</option> | |
| <option>Structural</option> | |
| </select></span> | |
| <label>SIFT:</label> | |
| <select id="selsift" onchange="reload();"> | |
| <option>All</option> | |
| <option>DAMAGING</option> | |
| <option>DAMAGING (Low)</option> | |
| <option>N/A</option> | |
| <option>Not scored</option> | |
| <option>TOLERATED</option> | |
| </select> | |
| <label>PPH2(Var):</label> | |
| <select id="selpph2var" onchange="reload();"> | |
| <option>All</option> | |
| <option>benign</option> | |
| <option>possibly damaging</option> | |
| <option>probably damaging</option> | |
| <option>unknown</option> | |
| </select> | |
| <label for="selpph">PPH2(Div):</label> | |
| <select id="selpph2div" onchange="reload();"> | |
| <option>All</option> | |
| <option>benign</option> | |
| <option>possibly damaging</option> | |
| <option>probably damaging</option> | |
| <option>unknown</option> | |
| </select> | |
| <label for="checkHQ">HQ</label> | |
| <input type="checkbox" id="checkHQ" checked="checked" onchange="reload();"/> | |
| </div> | |
| <div style="margin:10px;"> | |
| <svg:svg xmlns="http://www.w3.org/2000/svg" style="font-size:12px;stroke-width:1px;" width="100" height="100" id="main"> | |
| <svg:defs> | |
| <svg:linearGradient id="grad0" x1="50%" y1="0%" x2="50%" y2="100%"> | |
| <svg:stop offset="0%" style="stop-color:slategrey;"/> | |
| <svg:stop offset="100%" style="stop-color:lightblue;"/> | |
| </svg:linearGradient> | |
| <svg:linearGradient id="grad1" x1="50%" y1="0%" x2="50%" y2="100%"> | |
| <svg:stop offset="0%" style="stop-color:darkgray;"/> | |
| <svg:stop offset="50%" style="stop-color:white;"/> | |
| <svg:stop offset="100%" style="stop-color:darkgray;"/> | |
| </svg:linearGradient> | |
| <svg:linearGradient id="grad2" x1="50%" y1="0%" x2="50%" y2="100%"> | |
| <svg:stop offset="0%" style="stop-color:blue;"/> | |
| <svg:stop offset="50%" style="stop-color:white;"/> | |
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| </svg:linearGradient> | |
| </svg:defs> | |
| <svg:g id="mainG"/> | |
| </svg:svg> | |
| </div> | |
| <table width='100%' border="1" style='text-align:left;border-collapse:collapse;'> | |
| <caption id="Tcaption"></caption> | |
| <thead> | |
| <th>Position</th> | |
| <th>Ref</th> | |
| <th>Alt</th> | |
| <th>Depth</th> | |
| <th>RS##</th> | |
| <th>Sift</th> | |
| <th>PPH2(var)</th> | |
| <th>PPH2(div)</th> | |
| </thead> | |
| <tbody id="Tbody" style="height:300px; overflow: auto;"> | |
| </tbody> | |
| </table> | |
| </div> | |
| <hr/> | |
| <div style="font-size:10pt;"><a target="_blanck" href="http://plindenbaum.blogspot.com">Pierre Lindenbaum</a> PhD. (2010). <a href="mailto:[email protected]">[email protected]</a></div> | |
| </body> | |
| </html> |
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