Source for pseudoswitch lab-design generator

gistfile1.js

//
// Globals
//
var vrna = new LibVrna211;
var seq;
var constraint;

var t1 = 'GGAAA';
var t2 = 'GCUGAGCUUCGGCUCAGCA'
var t3 = 'AAAGAAACAACAACAACAAC';
var s1 = 'GAGCCCUGGGAGGCUC';
var s2 = 'GCUGUUCCCAGACAGC';

var h1ofs, h2ofs;

//
// Utilities
//
String.prototype.repeat = function (num)
{
  var a = [];
  a.length = (num << 0) + 1;
  return a.join(this);
};

function complement(base)
{
  if(base=='A') return 'U';
  if(base=='U') return 'A';
  if(base=='G') return 'C';
  if(base=='C') return 'G';
  return null;
}

//
// Start of code
//
do {
  var c1, c2, c3;
  clear();
  if( typeof sequence != 'undefined' ) {
    if( seq == sequence ) break;
    seq = sequence;
    // ...
    // determine c1,c2,c3,h1ofs,h2ofs from the sequence
    // ...
    h1ofs = seq.indexOf(s1);
    if( h1ofs == -1) break;
    c1 = h1ofs - 5;
    h2ofs = seq.indexOf(s2);
    if( h2ofs == -1) break;
    c2 = h2ofs - c1 - 21;
    c3 = 31 - c1 - c2;
    
  } else {
    c1 = Lib.random(11,13);
    c2 = Lib.random(5,6);
    c3 = 31 - c1 - c2;

    var x1 = Lib.randomSequence( c1 );
    h1ofs = t1.length + c1;
    var x2 = Lib.randomSequence( c2 );
    h2ofs = t1.length + c1 + s1.length + c2;
    var x3 = Lib.randomSequence( c3 );

    // randomize barcode
    var b = [];
    b[0] = Lib.randomSequenceWithBases(1,'GC');
    b[14] = complement(b[0]);
    for( j = 1; j <= 5; j++ ) {
      b[j] = Lib.randomSequence(1);
      b[14-j] = complement(b[j])
    }
    b[6] = Lib.randomSequenceWithBases(1,'CCG');
    b[8] = complement(b[0]);
    b[7] = "UUCG";
    b[15] = "A";
    t2 = b.join('');
    
    seq = t1+x1+s1+x2+s2+x3+t2+t3;
  }

  var ret = vrna.fold( seq );
  if( ret.mfe_structure.substr(0,5) != '.....' ) continue;
  if( ret.mfe_structure.substr(68,39) != '(((((((....))))))).....................' ) continue;
  if( ret.mfe_structure.substr(h1ofs,16) == '(((((......)))))' ) continue;
  if( ret.mfe_structure.substr(h2ofs,16) == '((((((....))))))' ) continue;
  var mfe_secstr = ret.mfe_structure;
  outln( seq );
  outln(ret.mfe_structure);
  outln(ret.free_energy);

  constraint = ".".repeat(h1ofs+5) + "xxxxxx" + ".".repeat(c2+10) + "xxxxxx" + ".".repeat(107-h2ofs-11);
  ret = vrna.foldWithConstraint( seq, constraint );
  if( ret.mfe_structure.substr(0,5) != '.....' ) continue;
  if( ret.mfe_structure.substr(68,39) != '(((((((....))))))).....................' ) continue;
  if( ret.mfe_structure.substr(h1ofs,16) != '(((((......)))))' ) continue;
  if( ret.mfe_structure.substr(h2ofs,16) != '(((((......)))))' ) continue;
  outln( constraint );
  outln(ret.mfe_structure);
  outln(ret.free_energy);

  constraint = ".".repeat(h1ofs+5) + "xxxxxx" + ".".repeat(107+c2+16-h2ofs-11);
  ret = vrna.foldWithConstraint( seq, constraint );
  if( ret.mfe_structure.substr(0,5) != '.....' ) continue;
  if( ret.mfe_structure.substr(68,39) != '(((((((....))))))).....................' ) continue;
  if( ret.mfe_structure.substr(h1ofs,16) != '(((((......)))))' ) continue;
  outln( constraint );
  outln(ret.mfe_structure);
  outln(ret.free_energy);

  constraint = ".".repeat(h1ofs+c2+21) + "xxxxxx" + ".".repeat(107-h2ofs-11);
  ret = vrna.foldWithConstraint( seq, constraint );
  if( ret.mfe_structure.substr(0,5) != '.....' ) continue;
  if( ret.mfe_structure.substr(68,39) != '(((((((....))))))).....................' ) continue;
  if( ret.mfe_structure.substr(h2ofs,16) != '(((((......)))))' ) continue;
  outln( constraint );
  outln(ret.mfe_structure);
  outln(ret.free_energy);

  constraint = ".".repeat(h1ofs+5) + "((((((" + ".".repeat(c2+10) + "))))))" + ".".repeat(107-h2ofs-11);
  ret = vrna.foldWithConstraint( seq, constraint );
  if( ret.mfe_structure == mfe_secstr ) continue;
  if( ret.mfe_structure.substr(0,5) != '.....' ) continue;
  if( ret.mfe_structure.substr(68,39) != '(((((((....))))))).....................' ) continue;
  outln( constraint );
  outln(ret.mfe_structure);
  outln(ret.free_energy);
  
  break;
  
} while(1);

delete vrna;
return null;