I am a fresh starter of Perl and I need to write a script that perform the same
function done by the following JavaScript. I know it is wrong to ask for code but I am
in urgent requirement of this.
The javascript code is as follows
<script language="JavaScript">
<!--
function transl()
{
translation = new
Array("cga","cgc","cgg","cgu","aga","agg","cua","cuc","cug","cuu","uua","uug","uca","ucc","ucg","ucu","agc","agu","aca","acc","acg","acu","cca","ccc","ccg","ccu","gca","gcc","gcg","gcu","gga","ggc","ggg","ggu","gua","guc","gug","guu","aaa","aag","aac","aau","caa","cag","cac","cau","gaa","gag","gac","gau","uac","uau","ugc","ugu","uuc","uuu","aua","auc","auu","aug","ugg","uaa","uag","uga");
treelett = new
Array("Arg","Arg","Arg","Arg","Arg","Arg","Leu","Leu","Leu","Leu","Leu","Leu","Ser","Ser","Ser","Ser","Ser","Ser","Thr","Thr","Thr","Thr","Pro","Pro","Pro","Pro","Ala","Ala","Ala","Ala","Gly","Gly","Gly","Gly","Val","Val","Val","Val","Lys","Lys","Asn","Asn","Gln","Gln","His","His","Glu","Glu","Asp","Asp","Tyr","Tyr","Cys","Cys","Phe","Phe","Ile","Ile","Ile","Met","Trp","Stop_ochre","Stop_amber","Stop_opal");
onelett = new
Array("r","r","r","r","r","r","l","l","l","l","l","l","s","s","s","s","s","s","t","t","t","t","p","p","p","p","a","a","a","a","g","g","g","g","v","v","v","v","k","k","n","n","q","q","h","h","e","e","d","d","y","y","c","c","f","f","i","i","i","m","w","*","*","*");
freq = new
Array("6.3","10.8","11.6","4.6","11.5","11.3","7.0","19.3","39.7","12.8","7.3","12.5","11.9","17.5","4.5","14.8","19.3","12.0","14.9","19.3","6.3","12.9","16.7","20.0","7.0","17.3","15.9","28.3","7.5","18.5","16.4","22.7","16.4","10.8","7.0","14.6","28.8","10.9","24.0","32.6","19.8","17.0","12.0","34.5","14.9","10.5","29.1","40.2","26.1","22.4","15.8","12.1","12.3","10.0","20.5","17.0","7.2","21.6","15.8","22.3","12.9","0.7","0.5","1.3",
"6.7","10.1","10.5","4.7","11.4","11.6","7.5","19.6","39.3","12.3","6.0","12.5","11.2","18.1","4.5","15.4","20.0","12.2","15.6","19.6","6.1","13.2","17.3","19.1","6.8","18.7","15.5","26.7","7.1","19.7","17.3","22.9","15.9","11.7","6.9","15.6","29.0","10.1","21.3","34.6","21.5","15.5","11.6","34.5","15.3","9.9","26.9","40.3","27.5","21.4","16.8","11.8","12.6","10.9","21.6","16.0","6.6","22.9","14.6","22.2","12.9","0.6","0.5","1.1",
"8.5","17.9","8.3","8.7","5.1","6.4","8.3","13.9","38.7","9.1","4.3","16.2","7.6","19.6","16.6","6.8","20.4","11.5","10.7","21.4","14.4","9.5","13.5","17.9","16.0","6.9","12.8","33.6","14.0","14.5","17.8","26.6","4.7","13.3","6.3","13.9","28.1","10.9","16.5","39.5","26.1","20.8","15.6","36.8","16.2","10.6","20.9","43.0","24.7","27.6","18.4","10.7","13.3","5.3","21.8","13.1","9.3","23.0","16.5","23.5","9.9","0.8","0.6","0.5",
"6.3","3.7","4.8","8.8","19.0","10.9","10.1","15.7","10.0","24.2","13.2","21.3","18.3","10.9","9.0","25.0","11.2","14.3","15.9","10.1","7.6","17.6","16.1","5.2","8.2","18.3","17.4","10.0","8.6","27.5","23.5","8.9","10.1","21.7","10.2","12.5","17.3","27.2","31.3","32.5","20.7","23.1","19.7","15.0","8.6","14.1","35.0","32.1","17.1","37.2","13.5","15.2","7.2","10.9","20.3","22.7","13.1","18.3","22.1","24.4","12.6","0.9","0.5","1.0",
"3.0","2.6","1.7","6.5","21.3","9.3","13.4","5.4","10.4","12.2","26.4","27.1","18.8","14.2","8.6","23.6","9.7","14.2","17.7","12.6","8.0","20.2","18.2","6.8","5.3","13.6","16.2","12.6","6.1","21.1","10.9","9.7","6.0","23.9","11.8","11.6","10.7","22.0","42.1","30.8","24.9","36.0","27.5","12.2","7.8","13.7","45.9","19.1","20.3","37.8","14.7","18.8","4.7","8.0","18.2","26.0","17.8","17.1","30.2","20.9","10.3","1.0","0.5","0.6",
"3.5","20.6","5.4","20.6","2.8","1.7","4.0","10.3","50.4","11.2","13.9","13.1","8.1","9.1","8.6","9.9","15.3","9.2","8.2","22.8","13.8","10.0","8.6","5.1","22.0","7.2","21.0","24.5","31.8","16.8","8.7","28.4","11.0","25.9","11.4","14.6","25.2","19.6","34.8","11.5","21.8","19.2","14.7","28.6","9.6","12.6","39.7","18.2","19.5","32.6","12.3","16.9","6.2","5.1","16.4","21.9","5.6","24.4","30.1","26.8","13.9","2.0","0.2","0.9");
organism = new Array("Homo sapiens","Mus musculus","Drosophila
melanogaster","Arabidopsis thaliana","Saccharomyces cerevisiae","Escherichia coli");
// забираем значения, заданные в форме
org = document.ftransl.org.selectedIndex;
str = document.ftransl.str.value;
r = parseFloat(document.ftransl.r.value);
if(isNaN(r)||r==0){alert("\"Critical frequency (per 1000)\" should be number.");
document.ftransl.r.focus(); return true;};
r = Math.abs(r);
document.ftransl.r.value = r;
name_seq = document.ftransl.s_name.value;
// приводим "str" к стандартному виду который будет называться "nseq"
nseq = ""
nseq = str.toLowerCase();
nseq = nseq.replace(/t/g,"u");
nseq = nseq.replace(/[^agcu]/g,"");
lnseq = nseq.length;
if(lnseq<3){alert("The sequence should be at least three nucleotides long.");
document.ftransl.str.focus(); return true;};
// транслируем нуклеотидную последовательность в номера, соответствующие
индивидуальным кодонам
aa = new Array()
prot = "<br> 1 ";
aalett = "";
codseq = "";
i3 = 0;
aalength = Math.floor(nseq.length/3);
while(i3<aalength) {
i3++; i4 = 0;
while(i4<64) {i4++; if(nseq.substring(i3*3-3,i3*3)==translation[i4-1]) {aa[i3-1] =
i4-1; break};}
}
i10 = 0;
while(i10<aalength) {i10++;
codseq =codseq + i10 + " -- "+ nseq.substring(i10*3-3,i10*3) + " -- " +
treelett[aa[i10-1]] + " -- " + freq[64*org+aa[i10-1]] + "\n";
t_letter = onelett[aa[i10-1]]
if(freq[64*org+aa[i10-1]]<r) {
t_letter = t_letter.toUpperCase();
t_letter = t_letter.bold();
t_letter = t_letter.fontcolor("red");
}
prot = prot + t_letter;
if(Math.floor(i10/10)*10==i10) {prot = prot +" "}
if(Math.floor(i10/50)*50==i10) {
p_str = i10+1
pp = Math.log(p_str)/Math.log(10);
prot = prot +"<br>"
for(i8=0;i8<5-pp;i8++) {prot = prot +" " };
prot = prot + p_str + " "}
}
document.ftransl.codseq.value = codseq;
id = window.open('','result',
config='height=500,width=600,toolbar=no,menubar=yes,scrollbars=yes,resizable=yes,location=no,status=no');
id.document.write("<title> Search of rear
codons </title><BODY BGCOLOR='white'>");
id.focus();
id.document.write("<h3>Brief results</h3><h4>Nucleotide sequence</h4><br><TT>");
id.document.write("> ");
id.document.write(name_seq);
id.document.write("<br><font color='Gray'>");
nstrings = Math.floor(nseq.length/50);
i_out = 0;
while(i_out<nstrings+1) {i_out++
id.document.write("<br>");
n_str = i_out*50-49
qq = Math.log(n_str)/Math.log(10);
for(i7=0;i7<5-qq;i7++) {id.document.write(" ")}
id.document.write(n_str);
id.document.write(" ");
for(i6=0;i6<5;i6++){
id.document.write(nseq.substring(50*i_out-50+10*i6,50*i_out-40+10*i6));
id.document.write(" ");
}
}
id.document.write("</TT></font><br> <br><h4>Amino acids sequence</h4><br>");
id.document.write("> ");
id.document.write(name_seq);
id.document.write(" ### translated in organism: ");
id.document.write(organism[org]);
id.document.write("<br><TT><font color='Gray'>");
id.document.write(prot);
id.document.write("</font></TT>");
id.document.write("<br><br><br><br><br><br><br><br><br>");
// закрываем окно
id.document.write("</body></html>");
id.document.close();
}
// -->
</script>
Thanks.
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