lindenb · January 15, 2014 20:16
diff --git a/pwm.html b/pwm.html
 <html>
 <head>
 <script type="text/javascript">
 //<![CDATA[

 /*  from R code https://github.com/genome-vendor/r-bioc-biostrings/blob/master/src/match_PWM.c */

 function compute_pwm_score(pwm, S,offset)
 	{
        var score=0.0;
 	var pwm_ncol = pwm[0].length;
        score = 0.00;
        for (var x = 0; x < pwm_ncol; x++)
        	{
                var y = -1;
                switch(S.charAt(offset+x))
                	{
                	case 'a':case 'A': y=0; break;
                	case 'c':case 'C': y=1; break;
                	case 't':case 'T': y=2; break;
                	case 'g':case 'G': y=3; break;
                	}
                if (y == -1) continue;
                score += pwm[y][x];
        	}
        return score;
 	}


 /* from R code */
 function match_PWM_XString(pwm,S,minscore)
 	{
 	var ncols= pwm[0].length;
 	
        for (var n1 = 0; n1+ncols<=S.length;++n1)
        	{
                var score = compute_pwm_score(pwm,S,n1);

                if (score >= minscore)
                        {
                        return score;
                        }
        	}
        return null;
 	}


 /* search pwm in dna */
 function scanPwm(matrix,dna,score)
 	{
 	var score=match_PWM_XString(matrix,dna,score);
 	var E=document.getElementById("rez3");
 	E.appendChild(document.createTextNode("Score(\""+dna+"\"): "+score+"\n"));
 	}


 /** convert a matrix to string */
 function matrixToString(matrix)
 	{
 	var s="";
 	var bases=["A","C","G","T"];
 	var i=0,j;
 	for(i=0;i< 4;++i)
 		{
 		var total=0;
 		s+=bases[i];
 		for(j=0;j< matrix[i].length;++j)
 			{
 			s+=" "+matrix[i][j];
 			total+=matrix[i][j];
 			}
 		//s+=" ("+total+")";
 		s+="\n";
 		}
 	return s;
 	}

 function run()
 	{
 	/* example from http://davetang.org/muse/2013/10/01/position-weight-matrix/ */
 	var pfm= [
 		[0, 4, 4, 0, 3, 7, 4, 3, 5, 4, 2, 0, 0, 4],/* A */
 		[3, 0, 4, 8, 0, 0, 0, 3, 0, 0, 0, 0, 2, 4],/* C */
 		[2, 3, 0, 0, 0, 0, 0, 0, 1, 0, 6, 8, 5, 0],/* G */
 		[3, 1, 0, 0, 5, 1, 4, 2, 2, 4, 0, 0, 1, 0] /* T */
 		];
 	var ncols= pfm[0].length;
 	var pwm= [
 		new Array(ncols),
 		new Array(ncols),
 		new Array(ncols),
 		new Array(ncols)
 		];

 	
 	/* convert pfm to pwm */
 	for(var x=0;x<ncols;++x)
 		{
 		var total=0;
 		for(var y=0;y<4;++y) total+=pfm[y][x];
 		for(var y=0;y<4;++y)
 			{
 			var prob_base=0.25;
 			var freq=pfm[y][x];
 			var w= Math.log2 ( ( freq + Math.sqrt(total) * prob_base ) / ( total + Math.sqrt(total) ) / prob_base );
  			pwm[y][x]=w;
 			}
 		}
 	
 	var E=document.getElementById("rez1");
 	E.appendChild(document.createTextNode(matrixToString(pfm)));
 	E=document.getElementById("rez2");
 	E.appendChild(document.createTextNode(matrixToString(pwm)));	
 	
 	/* search this pattern */
 	var min_score=0.8;
 	scanPwm(pwm,"GAAATTACAAGGG",min_score);
 	scanPwm(pwm,"ttacataagtagtc",min_score);
 	scanPwm(pwm,"ttacataACCagtc",min_score);
 	scanPwm(pwm,"CAACTAAAAAGGGC",min_score);
 	}

 //]]>
 </script>
 </head>
 <body onload="run()">
 <h3>PFM</h3>
 <pre id="rez1"></pre>
 <h3>PWM</h3>
 <pre id="rez2"></pre>
 <h3>Search</h3>
 <pre id="rez3"></pre>
 </body>
 </html>
	<html>
	<head>
	<script type="text/javascript">
	//<![CDATA[

	/* from R code https://github.com/genome-vendor/r-bioc-biostrings/blob/master/src/match_PWM.c */

	function compute_pwm_score(pwm, S,offset)
	{
	var score=0.0;
	var pwm_ncol = pwm[0].length;
	score = 0.00;
	for (var x = 0; x < pwm_ncol; x++)
	{
	var y = -1;
	switch(S.charAt(offset+x))
	{
	case 'a':case 'A': y=0; break;
	case 'c':case 'C': y=1; break;
	case 't':case 'T': y=2; break;
	case 'g':case 'G': y=3; break;
	}
	if (y == -1) continue;
	score += pwm[y][x];
	}
	return score;
	}


	/* from R code */
	function match_PWM_XString(pwm,S,minscore)
	{
	var ncols= pwm[0].length;

	for (var n1 = 0; n1+ncols<=S.length;++n1)
	{
	var score = compute_pwm_score(pwm,S,n1);

	if (score >= minscore)
	{
	return score;
	}
	}
	return null;
	}


	/* search pwm in dna */
	function scanPwm(matrix,dna,score)
	{
	var score=match_PWM_XString(matrix,dna,score);
	var E=document.getElementById("rez3");
	E.appendChild(document.createTextNode("Score(\""+dna+"\"): "+score+"\n"));
	}


	/** convert a matrix to string */
	function matrixToString(matrix)
	{
	var s="";
	var bases=["A","C","G","T"];
	var i=0,j;
	for(i=0;i< 4;++i)
	{
	var total=0;
	s+=bases[i];
	for(j=0;j< matrix[i].length;++j)
	{
	s+=" "+matrix[i][j];
	total+=matrix[i][j];
	}
	//s+=" ("+total+")";
	s+="\n";
	}
	return s;
	}

	function run()
	{
	/* example from http://davetang.org/muse/2013/10/01/position-weight-matrix/ */
	var pfm= [
	[0, 4, 4, 0, 3, 7, 4, 3, 5, 4, 2, 0, 0, 4],/* A */
	[3, 0, 4, 8, 0, 0, 0, 3, 0, 0, 0, 0, 2, 4],/* C */
	[2, 3, 0, 0, 0, 0, 0, 0, 1, 0, 6, 8, 5, 0],/* G */
	[3, 1, 0, 0, 5, 1, 4, 2, 2, 4, 0, 0, 1, 0] /* T */
	];
	var ncols= pfm[0].length;
	var pwm= [
	new Array(ncols),
	new Array(ncols),
	new Array(ncols),
	new Array(ncols)
	];


	/* convert pfm to pwm */
	for(var x=0;x<ncols;++x)
	{
	var total=0;
	for(var y=0;y<4;++y) total+=pfm[y][x];
	for(var y=0;y<4;++y)
	{
	var prob_base=0.25;
	var freq=pfm[y][x];
	var w= Math.log2 ( ( freq + Math.sqrt(total) * prob_base ) / ( total + Math.sqrt(total) ) / prob_base );
	pwm[y][x]=w;
	}
	}

	var E=document.getElementById("rez1");
	E.appendChild(document.createTextNode(matrixToString(pfm)));
	E=document.getElementById("rez2");
	E.appendChild(document.createTextNode(matrixToString(pwm)));

	/* search this pattern */
	var min_score=0.8;
	scanPwm(pwm,"GAAATTACAAGGG",min_score);
	scanPwm(pwm,"ttacataagtagtc",min_score);
	scanPwm(pwm,"ttacataACCagtc",min_score);
	scanPwm(pwm,"CAACTAAAAAGGGC",min_score);
	}

	//]]>
	</script>
	</head>
	<body onload="run()">
	<h3>PFM</h3>
	<pre id="rez1"></pre>
	<h3>PWM</h3>
	<pre id="rez2"></pre>
	<h3>Search</h3>
	<pre id="rez3"></pre>
	</body>
	</html>