bio parser.js

peptide = '1MKLHYVAVLTLAILMFLTWLPESLSCNKALCASDVSKCLIQELCQCRPGEGNCACCKECM6061LCLGALWDECCDCVGMCNPRNYADTPPTSKSTVEELHEPIPSLFRALTEGDTQLNWNIVS120121FPVAEELSHHENLVSFLETVNQPHHQNVSVPSNNVHAPYSSDKEHMCTVVYFDDCMSIHQ180181CKISCESMGASKYRWFHNACCECIGPECIDYGSKTVKCMNCMF223'.match(/[a-zA-Z]/g).join('');
dna = '1CGGCGGGAGGCGCGGCCTGGCCTCGCACTCAAAGCCGCCGCAGCGCGCCCCGGGCTCGGC60 61CGACCCGGCGGGGATCTAGGGGTGGGCGACTTCGCGGGACCGTGGCGCATGTTTCCTGGG120 121AGTTACTGATCATCTTCTTTGAAGAAACATGAAGTTACACTATGTTGCTGTGCTTACTCT180 181AGCCATCCTGATGTTCCTGACATGGCTTCCAGAATCACTGAGCTGTAACAAAGCACTCTG240 241TGCTAGTGATGTGAGCAAATGCCTCATTCAGGAGCTCTGCCAGTGCCGGCCGGGAGAAGG300 301CAATTGCGCCTGCTGTAAGGAGTGCATGCTGTGTCTTGGGGCCCTTTGGGACGAGTGCTG360 361TGACTGTGTTGGTATGTGTAATCCTCGAAATTATAGTGACACACCTCCAACTTCAAAGAG420 421CACAGTGGAGGAGCTGCATGAACCGATCCCTTCTCTCTTCCGGGCACTCACAGAAGGAGA480 481TACTCAGTTGAATTGGAACATCGTTTCTTTCCCTGTTGCAGAAGAACTTTCACATCATGA540 541GAATCTGGTTTCATTTTTAGAAACTGTGAACCAGCCACACCACCAGAATGTGTCTGTCCC600 601CAGCAATAATGTTCACGCGCCTTATTCCAGTGACAAAGAACACATGTGTACTGTGGTTTA660 661TTTTGATGACTGCATGTCCATACATCAGTGTAAAATATCCTGTGAGTCCATGGGAGCATC720 721CAAATATCGCTGGTTTCATAATGCCTGCTGCGAGTGCATTGGTCCAGAATGTATTGACTA780 781TGGTAGTAAAACTGTCAAATGTATGAACTGCATGTTTTAAAGAAGACAAATGCAAACCAA840 841AGCAACTTAGTAAAATAATAGGTATAAAAAGTTATTCTGTAAGTCTGTTGGTTGTATCTT900 901GTATCAGAATCCCAGTAAGTTAAGTTGTAAAGACTTTGGAATAAGTTTCTTTTAAAAATA960 961TGACATAGCCAGTGATGTGTTTAATTATATAACTGTTCTT1000'.match(/[a-zA-Z]/g).join('');

code = prompt('Insert codon table');

startCodon = "ATG";

var startList = [];
for (i=0;i<dna.match(/ATG/g).length;i++) {
  if (i===0) {
    startList.push(dna.indexOf("ATG"));
  }
  else startList.push(startList[i-1]+dna.substr(startList[i-1]+3).indexOf("ATG"));
}

// the ORFs somehow start 3 bases early?? use .substr(3)...

function ORF(orf,at)
{
this.orf=orf;
this.at=at;
this.len=orf.length;
}

var ORFlist = [];
for (i=0;i<startList.length;i++) {
  newORF = dna.substr(startList[i]);
  ORFlist.push(new ORF(newORF,startList[i]));
}

function PTM(ptm,at)
{
this.ptm=ptm;
this.at=at;
this.len=ptm.length;
}

var PTMlist = [];
var PTMtarget = /N.[ST]/g; // for NX(ST)
for (i=0;i<peptide.match(PTMtarget).length;i++) {
    newPTM = peptide.match(PTMtarget)[0];
    PTMlist.push(new PTM(newPTM,peptide.indexOf(newPTM)));
}

// for now just confirm with Rubular that there's only 1 matching PTM consensus site

theORF = ORFlist[1].orf.substr(3);
signal = theORF.substr(0,25*3);

function codonFor(residueAt) {
  return theORF.substr(residueAt*3,3)+" at "+residueAt*3;
}


////////////////////////////////////////////////////////////////////

singles = code.match(/ [(].[)]/g);

function Codon(letter,codon,residue) {
  this.letter = letter;
  this.codon = codon;
  this.residue = residue;
}

var shortList = [];
for (i=0;i<code.match(/[A-Z][A-Z][A-Z]/g).length;i++) {
  if (code[code.indexOf(code.match(/[A-Z][A-Z][A-Z]/g)[i])+7] == 'p') {
      var short = code.substr(code.indexOf(code.match(/[A-Z][A-Z][A-Z]/g)[i])+4,4);
  }
  else var short = code.substr(code.indexOf(code.match(/[A-Z][A-Z][A-Z]/g)[i])+4,3);
  shortList.push(short);
}

var codonList = [];
for (i=0;i<code.match(/[A-Z][A-Z][A-Z]/g).length;i++) {
  var short = code.substr(code.indexOf(code.match(/[A-Z][A-Z][A-Z]/g)[i]),3);
  codonList.push(short);
}

var letters = [];
for (i=0;i<code.match(/[A-Z][A-Z][A-Z]/g).length;i++) {
  if (shortList[i] == "Stop") {
    letters.push("—");
  }
  else if (code[code.indexOf(code.match(/[A-Z][A-Z][A-Z]/g)[i])+8] == "(") {
    letters.push(code[code.indexOf(code.match(/[A-Z][A-Z][A-Z]/g)[i])+9]);
  }
  else letters.push(letters[i-1]);
}

myTable = [];
for (i=0;i<codonList.length;i++) {
  var newCodon = new Codon(letters[i],codonList[i],shortList[i]);
  myTable.push(newCodon);
  console.log(newCodon);
}

// var codons = theORF.match(/.{1,3}/g);
var realORF = theORF.substring(0,223*3);
var codons = realORF.match(/.{1,3}/g);

function ResToCodon(residue) {
  var results = [];
  for (i=0;i<myTable.length;i++) {
    if (myTable[i].residue == residue) {
      thisCodon = myTable[i].codon;
      results.push(thisCodon);
    }
  } return results;
}

var stopCodons = ResToCodon("Stop");

for (i=0;i<codons.length;i++) {
codons[i] == stopCodons;
}

function LetterToCodon(letter) {
  var results = [];
  for (i=0;i<myTable.length;i++) {
    if (myTable[i].letter == letter) {
      thisCodon = myTable[i].codon;
      results.push(thisCodon);
    }
  } return results;
}

function LetterToRes(letter) {
  var results = [];
  for (i=0;i<myTable.length;i++) {
    if (myTable[i].letter == letter) {
      thisCodon = myTable[i].codon;
      results.push(thisCodon);
    }
  }
}

function ResToLetter(residue) {
  for (i=0;i<myTable.length;i++) {
    if (myTable[i].residue == residue) return myTable[i].letter;
  }
}

function CodonToRes(codon) {
  for (i=0;i<myTable.length;i++) {
    if (myTable[i].codon == codon) return myTable[i].residue;
  }
}

function CodonToLetter(codon) {
  for (i=0;i<myTable.length;i++) {
    if (myTable[i].codon == codon) return myTable[i].letter;
  }
}

function translate(seq) { // for a nucleotide sequence split into an array of 3mers
  var translation = [];
  for (i=0;i<seq.length;i++) {
    translation.push(CodonToLetter(seq[i]));
  }
  return translation;
}

// Find the stop codons

function stop(atCodon)
{
this.orf=theORF.substr(0,(atCodon-1)*3);
this.at=atCodon;
this.len=this.orf.length;
}

var allORFs = [];
for (i=0;i<codons.length;i++) {
  if (codons[i] == stopCodons[0] || codons[i] == stopCodons[1] || codons[i] == stopCodons[2]) {
    var newbie = new stop(i);
    allORFs.push(newbie);
  }
}

var transcripts = [];
for (r=0;r<allORFs.length;r++) {
  transcript = translate(allORFs[r].orf.match(/.{1,3}/g));
  transcripts.push(transcript); // must be in 3mers to translate!
}

if (typeof String.prototype.editAt !== 'function') {
String.prototype.editAt = function(index,mut) {
  return this.substr(0,index)+mut+this.substr(index+1,this.length);
};
}

mutORF = theORF.editAt(439,"C"); // 439A>C
mutCodons = mutORF.match(/.{1,3}/g);

// code from previous tutorial, when var seq = 'GGGGCCCTTTGGGACGAGTGCTGTGACTGTGTTGG';

var seq = mutORF;
var mismatch = 1;
var GCcount = seq.match(/[GC]/g).length;
var GCper = GCcount/seq.length*100;
var Tm = 81.5+(0.41*GCper)-(675/seq.length)-mismatch/seq.length;
console.log(Tm);
anti = seq.replace(/G/g,'c').replace(/C/g,'g').replace(/A/g,'t').replace(/T/g,'a').toUpperCase();

/*

This kills consoles :-(

translation = [];
translate(realORF.match(/.{1,3}/g));
var realTranscript = translation.join('');

*/

codonUsageRegEx = /[A-Z]{3}\s{8,9}\d{1,2}\.\d\d\s{8,9}\d{1,2}\.\d\d\s{8,9}\d{1,2}\.\d\d/g;
codonRegEx = /^[A-Z]{3}/;
usageRegEx = /\d\.\d\d$/;
// Input from geneinfinity.org/sms/sms_codonusage.html
// usageTable = prompt().match(codonUsageRegEx);

function codonUsage(codon,usage)
{
this.codon=codon;
this.usage=usage;
}

codonDB = [];
for (b=0;b<usageTable.length;b++) {
  var usageCodon = usageTable[b].match(codonRegEx)[0];
  var usagePer = Math.round((theORF.match(usageTable[b].match(codonRegEx)).length/theORF.length)*10000)/100;
  var newUsage = new codonUsage(usageCodon,usagePer);
  codonDB.push(newUsage);
}

// Codon Usage Tabulated from GenBank tables at kazusa.or.jp/codon

CUTGregex = /[A-Z]{3}\s+\d+\.\d\(\s+\d+\)/g;
CUTusageRegEx = /\d{1,2}\.\d/;

K12table = prompt().match(CUTGregex); // kazusa.or.jp/codon/cgi-bin/showcodon.cgi?species=83333

K12DB = [];
for (b=0;b<usageTable.length;b++) {
  var newUsage = new codonUsage(K12table[b].match(codonRegEx)[0].replace(/U/g,'T'),Math.round(K12table[b].match(CUTusageRegEx)[0])/1000);
  K12DB.push(newUsage);
}

function usageComp(codon,usage1,usage2)
{
this.codon=codon;
this.usage1=usage1;
this.usage2=usage2;
}

function compareUsage(DB1,DB2) {
  for (z=0;z<DB1.length;z++) {
    for (d=0;d<DB2.length;d++) {
      if (DB1[z].codon == DB2[d].codon) {
        var newComp = new usageComp(DB1[z].codon,DB1[z].usage,DB2[d].usage);
        compResults.push(newComp);
      }
    }
  }
}

// This is comparing chalk with cheese, as the usage info for the protein are relative to other codons for the same AA
// To compare properly, take the relative uses of different amino acids! This was done for stop codons already
// That is, construct a new variable each time you want to use the codons, containing var ResToCodon(<Codon 3 letter code>);

// I don't have time to make this, commented out below is the basic structure of a parser for such a table. Divide each K12 codon by total of others' uses.

function codonRatesFor(res) {
for (i=0;i<K12DB.length;i++) {
    if (ResToCodon(res).join().match(K12DB[i].codon) !== null) {
      console.log(K12DB[i].codon+" "+K12DB[i].usage);
    }
  }
}

// E.g. for Thr codonRatesFor('Thr') ACT 0.008 + ACC 0.023 + ACA 0.006 + ACG 0.012 = 0.049
// 

/*

compResults = [];
compareUsage(codonDB,K12DB);

for (i=0;i<compResults.length;i++) {
  if (compResults[i].usage1 != "0.00") {
  console.log(compResults[i].codon+"\t"+compResults[i].usage1+"\t"+compResults[i].usage2);
  }
}

*/

for (i=0;i<compResults.length;i++) {
  if (Math.abs(compResults[i].usage1-compResults[i].usage2) > 0.5 && compResults[i].usage2 < 0.1) {
  console.log(compResults[i].codon+"\t"+compResults[i].usage1+"\t"+compResults[i].usage2);
  }
}

/*

 GCG         1.00         4.48         0.09 
Ala      GCA         4.00        17.94         0.36 
Ala      GCT         2.00         8.97         0.18 
Ala      GCC         4.00        17.94         0.36 

Cys      TGT        12.00        53.81         0.50 
Cys      TGC        12.00        53.81         0.50 

Asp      GAT         3.00        13.45         0.33 
Asp      GAC         6.00        26.91         0.67 

Glu      GAG         8.00        35.87         0.47 
Glu      GAA         9.00        40.36         0.53 

Phe      TTT         4.00        17.94         0.57 
Phe      TTC         3.00        13.45         0.43 

Gly      GGG         1.00         4.48         0.13 
Gly      GGA         3.00        13.45         0.38 
Gly      GGT         3.00        13.45         0.38 
Gly      GGC         1.00         4.48         0.13 

His      CAT         5.00        22.42         0.50 
His      CAC         5.00        22.42         0.50 

Ile      ATA         2.00         8.97         0.25 
Ile      ATT         3.00        13.45         0.38 
Ile      ATC         3.00        13.45         0.38 

Lys      AAG         3.00        13.45         0.30 
Lys      AAA         7.00        31.39         0.70 

Leu      TTG         1.00         4.48         0.05 
Leu      TTA         2.00         8.97         0.10 
Leu      CTG         6.00        26.91         0.30 
Leu      CTA         1.00         4.48         0.05 
Leu      CTT         5.00        22.42         0.25 
Leu      CTC         5.00        22.42         0.25 

Met      ATG         9.00        40.36         1.00 

Asn      AAT         9.00        40.36         0.69 
Asn      AAC         4.00        17.94         0.31 

Pro      CCG         2.00         8.97         0.17 
Pro      CCA         4.00        17.94         0.33 
Pro      CCT         5.00        22.42         0.42 
Pro      CCC         1.00         4.48         0.08 

Gln      CAG         6.00        26.91         1.00 
Gln      CAA         0.00         0.00         0.00 

Arg      AGG         0.00         0.00         0.00 
Arg      AGA         0.00         0.00         0.00 
Arg      CGG         2.00         8.97         0.50 
Arg      CGA         1.00         4.48         0.25 
Arg      CGT         0.00         0.00         0.00 
Arg      CGC         1.00         4.48         0.25 

Ser      AGT         4.00        17.94         0.20 
Ser      AGC         4.00        17.94         0.20 
Ser      TCG         0.00         0.00         0.00 
Ser      TCA         4.00        17.94         0.20 
Ser      TCT         3.00        13.45         0.15 
Ser      TCC         5.00        22.42         0.25 

Thr      ACG         0.00         0.00         0.00 
Thr      ACA         4.00        17.94         0.40 
Thr      ACT         6.00        26.91         0.60 
Thr      ACC         0.00         0.00         0.00 

Val      GTG         6.00        26.91         0.40 
Val      GTA         0.00         0.00         0.00 
Val      GTT         7.00        31.39         0.47 
Val      GTC         2.00         8.97         0.13 

Trp      TGG         4.00        17.94         1.00 

Tyr      TAT         6.00        26.91         1.00 
Tyr      TAC         0.00         0.00         0.00 

End      TGA         0.00         0.00         0.00 
End      TAG         0.00         0.00         0.00 
End      TAA         0.00         0.00         0.00 

*/

/*

TTT Phe (F)
TTC Phe
TTA Leu (L)
TTG Leu
TCT Ser (S)
TCC Ser
TCA Ser
TCG Ser
TAT Tyr (Y)
TAC Tyr
TAA Stop
TAG Stop
TGT Cys (C)
TGC Cys
TGA Stop
TGG Trp (W)
CTT Leu (L)
CTC Leu
CTA Leu
CTG Leu
CCT Pro (P)
CCC Pro
CCA Pro
CCG Pro
CAT His (H)
CAC His
CAA Gln (Q)
CAG Gln
CGT Arg (R)
CGC Arg
CGA Arg
CGG Arg
ATT Ile (I)
ATC Ile
ATA Ile
ATG Met (M)
ACT Thr (T)
ACC Thr
ACA Thr
ACG Thr
AAT Asn (N)
AAC Asn
AAA Lys (K)
AAG Lys
AGT Ser (S)
AGC Ser
AGA Arg (R)
AGG Arg
GTT Val (V)
GTC Val
GTA Val
GTG Val
GCT Ala (A)
GCC Ala
GCA Ala
GCG Ala
GAT Asp (D)
GAC Asp
GAA Glu (E)
GAG Glu
GGT Gly (G)
GGC Gly
GGA Gly
GGG Gly

*/