2nd Bioinformatic Coding Problem: genes into protein primary structures

Question

On this wiki page:
https://wiki.sdn.sap.com/wiki/display/EmTech/Bio-InformaticBasicsInRelationtoScriptingLanguages
Post 3  (Protein Primary Structures from a Scripting Language Point of Vew ) presents the background needed to understand how to translate a protein gene like this:
atgaacaaacagatcgatctacccattgctgatgtacaaggctcgttggacacaagacat
attgccatcgacagagtaggaatcaaagcgatccggcatcctgtcgtggtggcagataaa
ggcggtggctcccagcataccgtggcgcaattcaatatgtacgtcaatctgccccacaac
ttcaagggaacccacatgtctcgctttgtcgagatactgaacagtcacgagcgcgagatt
tcggtcgaatcgttcgaggaaatcctgcgttccatggtcagcagactggaatcggattcc
ggacatatcgaaatggccttcccttacttcatcaataaatctgcacctgtctcgggtgta
aaaagcctgctggactacgaagtgacatttatcggtgagatcaaacacggcaatcaatat
agttttaccatgaaggtaatcgtccctgttaccagcctgtgcccctgctccaaaaaaata
tccgactacggtgcacacaaccagcgttcacatgtcacgatttcggtgcgtaccaatagt
ttcatctggatcgaggacatcatcagaatcgcggaagagcaggcctcatgcgaactgtac
ggcctgctgaaacgcccggatgaaaaatatgttacggaaagagcttacaacaatccgaaa
tttgtcgaagatatcgtccgcgatgtggccgaagtactcaaccacgatgaccgtatagac
gcctatatcgttgaatcagaaaatttcgaatccatacacaaccactctgcctacgcattg
atcgaacgagacaaaagaatacgataa
into a protein primary structure like this:
MNKQIDLPIADVQGSLDTRHIAIDRVGIKAIRHPVVVADKGGGSQHTVAQFNMYVNLPHNFKGTHMSRFV
EILNSHEREISVESFEEILRSMVSRLESDSGHIEMAFPYFINKSAPVSGVKSLLDYEVTFIGEIKHGNQY
SFTMKVIVPVTSLCPCSKKISDYGAHNQRSHVTISVRTNSFIWIEDIIRIAEEQASCELYGLLKRPDEKY
VTERAYNNPKFVEDIVRDVAEVLNHDDRIDAYIVESENFESIHNHSAYALIERDKRIR
using the "standard genetic code":
F: ttt  S: tct  Y: tat  C: tgt 
F: ttc  S: tcc  Y: tac  C: tgc 
L: tta  S: tca  *: taa  *: tga 
L: ttg  S: tcg: *: tag  W: tgg 
L: ctt  P: cct  H: cat  R: cgt 
L: ctc  P: ccc  H: cac  R: cgc 
L: cta  P: cca  Q: caa  R: cga 
L: ctg  P: ccg  Q: cag  R: cgg 
I: att  T: act  N: aat  S: agt 
I: atc  T: acc  N: aac  S: agc 
I: ata  T: aca  K: aaa  R: aga 
M: atg  T: acg  K: aag  R: agg 
V: gtt  A: gct  D: gat  G: ggtr 
V: gtc  A: gcc  D: gac  G: ggc 
V: gta  A: gca  E: gaa  G: gga 
V: gtg  A: gcg  E: gag  G: ggg 
I'd love to have a copy of the necessary translation routine in each of the usual scripting languages - any routines posted in this thread will be added to the above wiki page.

Answer 1

$inseq  = "atgaacaaacagatcgatctacccattgctgatgtacaaggctcgttggacacaagacat";
$inseq .= "attgccatcgacagagtaggaatcaaagcgatccggcatcctgtcgtggtggcagataaa";
$inseq .= "ggcggtggctcccagcataccgtggcgcaattcaatatgtacgtcaatctgccccacaac";
$inseq .= "ttcaagggaacccacatgtctcgctttgtcgagatactgaacagtcacgagcgcgagatt";
$inseq .= "tcggtcgaatcgttcgaggaaatcctgcgttccatggtcagcagactggaatcggattcc";
$inseq .= "ggacatatcgaaatggccttcccttacttcatcaataaatctgcacctgtctcgggtgta";
$inseq .= "aaaagcctgctggactacgaagtgacatttatcggtgagatcaaacacggcaatcaatat";
$inseq .= "agttttaccatgaaggtaatcgtccctgttaccagcctgtgcccctgctccaaaaaaata";
$inseq .= "tccgactacggtgcacacaaccagcgttcacatgtcacgatttcggtgcgtaccaatagt";
$inseq .= "ttcatctggatcgaggacatcatcagaatcgcggaagagcaggcctcatgcgaactgtac";
$inseq .= "ggcctgctgaaacgcccggatgaaaaatatgttacggaaagagcttacaacaatccgaaa";
$inseq .= "tttgtcgaagatatcgtccgcgatgtggccgaagtactcaaccacgatgaccgtatagac";
$inseq .= "gcctatatcgttgaatcagaaaatttcgaatccatacacaaccactctgcctacgcattg";
$inseq .= "atcgaacgagacaaaagaatacgataa";
$trans  = array(
"ttt" => "F", "ctt" => "L", "att" => "I", "gtt" => "V",
"ttc" => "F", "ctc" => "L", "atc" => "I", "gtc" => "V",
"tct" => "S", "cta" => "L", "ata" => "I", "gta" => "V",
"tcc" => "S", "ctg" => "L", "atg" => "M", "gtg" => "V",
"tca" => "S", "cct" => "P", "act" => "T", "gct" => "A",
"tcg" => "S", "ccc" => "P", "acc" => "T", "gcc" => "A",
"tta" => "L", "cca" => "P", "aca" => "T", "gca" => "A",
"ttg" => "L", "ccg" => "P", "acg" => "T", "gcg" => "A",
"tat" => "Y", "cat" => "H", "aat" => "N", "gat" => "D",
"tac" => "Y", "cac" => "H", "aac" => "N", "gac" => "D",
"tgt" => "C", "caa" => "Q", "aaa" => "K", "gaa" => "E",
"tgc" => "C", "cag" => "Q", "aag" => "K", "gag" => "E",
"tgg" => "W", "cgt" => "R", "agt" => "S", "ggt" => "G",
"taa" => "*", "cgc" => "R", "agc" => "S", "ggc" => "G",
"tga" => "*", "cga" => "R", "aga" => "R", "gga" => "G",
"tag" => "*", "cgg" => "R", "agg" => "R", "ggg" => "G");
$inseq = strtr($inseq, "u", "t");
$substring_length[0] = -1; $stops[0] = "taa";
$substring_length[1] = -1; $stops[1] = "tga";
$substring_length[2] = -1; $stops[2] = "tag";
$i = 0;
foreach($substring_length as $sl){
  $substring_length[$i] = strlen($inseq);
  while($sl % 3 <> 0 && $sl <= strlen($inseq)){
    $sl = strpos($inseq, $stops[$i], $sl+1);
  if(!$sl === false){
    $substring_length[$i] = $sl;
  $i++;
echo strtr(substr($inseq, 0, min($substring_length)),$trans);
most of the code (apart from the definition of the input parameters) is an attempt to efficiently find the first stop codon to avoid loading and translating a sequence of several kilobytes where actually the first stop codon appears after a few bytes; if this isn't necessary the actual algorithm is a one-liner.
the language is of course ... well, a little trivial riddle (google some keywords to find out).