update: DNA, RNA what's the difference? My original code used the cDNA, not the mRNA. I changed it and reran it, and everyone's code now works except for japhy's.

OK, this is going to be a long one...

I was going to benchmark these golf examples to see which one was fastest, but there seems to be some cheating going on. Honestly, I don't really understand what any of these is doing, so I don't know if the cheating was intentional or not. To do the benchmarking, was was going to use the CFTR mRNA (that is the protein that, when mutated, causes cystic fibrosis). The mRNA (with leading and trailing sequence removed) is in the __DATA__ section of the code. The correct translation looks like this:

MQRSPLEKASVVSKLFFSWTRPILRKGYRQRLELSDIYQIPSVDSADNLSEKLEREWDRELASKKNPKLI
+NALRRCFFWRFMFYGIFLYLGEVTKAVQPLLLGRIIASYDPDNKEERSIAIYLGIGLCLLFIVRTLLLH
+PAIFGLHHIGMQMRIAMFSLIYKKTLKLSSRVLDKISIGQLVSLLSNNLNKFDEGLALAHFVWIAPLQV
+ALLMGLIWELLQASAFCGLGFLIVLALFQAGLGRMMMKYRDQRAGKISERLVITSEMIENIQSVKAYCW
+EEAMEKMIENLRQTELKLTRKAAYVRYFNSSAFFFSGFFVVFLSVLPYALIKGIILRKIFTTISFCIVL
+RMAVTRQFPWAVQTWYDSLGAINKIQDFLQKQEYKTLEYNLTTTEVVMENVTAFWEEGFGELFEKAKQN
+NNNRKTSNGDDSLFFSNFSLLGTPVLKDINFKIERGQLLAVAGSTGAGKTSLLMMIMGELEPSEGKIKH
+SGRISFCSQFSWIMPGTIKENIIFGVSYDEYRYRSVIKACQLEEDISKFAEKDNIVLGEGGITLSGGQR
+ARISLARAVYKDADLYLLDSPFGYLDVLTEKEIFESCVCKLMANKTRILVTSKMEHLKKADKILILNEG
+SSYFYGTFSELQNLQPDFSSKLMGCDSFDQFSAERRNSILTETLHRFSLEGDAPVSWTETKKQSFKQTG
+EFGEKRKNSILNPINSIRKFSIVQKTPLQMNGIEEDSDEPLERRLSLVPDSEQGEAILPRISVISTGPT
+LQARRRQSVLNLMTHSVNQGQNIHRKTTASTRKVSLAPQANLTELDIYSRRLSQETGLEISEEINEEDL
+KECLFDDMESIPAVTTWNTYLRYITVHKSLIFVLIWCLVIFLAEVAASLVVLWLLGNTPLQDKGNSTHS
+RNNSYAVIITSTSSYYVFYIYVGVADTLLAMGFFRGLPLVHTLITVSKILHHKMLHSVLQAPMSTLNTL
+KAGGILNRFSKDIAILDDLLPLTIFDFIQLLLIVIGAIAVVAVLQPYIFVATVPVIVAFIMLRAYFLQT
+SQQLKQLESEGRSPIFTHLVTSLKGLWTLRAFGRQPYFETLFHKALNLHTANWFLYLSTLRWFQMRIEM
+IFVIFFIAVTFISILTTGEGEGRVGIILTLAMNIMSTLQWAVNSSIDVDSLMRSVSRVFKFIDMPTEGK
+PTKSTKPYKNGQLSKVMIIENSHVKKDDIWPSGGQMTVKDLTAKYTEGGNAILENISFSISPGQRVGLL
+GRTGSGKSTLLSAFLRLLNTEGEIQIDGVSWDSITLQQWRKAFGVIPQKVFIFSGTFRKNLDPYEQWSD
+QEIWKVADEVGLRSVIEQFPGKLDFVLVDGGCVLSHGHKQLMCLARSVLSKAKILLLDEPSAHLDPVTY
+QIIRRTLKQAFADCTVILCEHRIEAMLECQQFLVIEENKVRQYDSIQKLLNERSLFRQAISPSDRVKLF
+PHRNSSKCKSKPQIAALKEETEEEVQDTRL.
[download]

However, tachyon's, MeowChow's and tadman's orignal codes all gave this:

QRPEKASKSTRPRKGRQREDQPADEKEREREAKKPKARRRGGETKAQPGRADPNKEERAGGRTHPAGHGQ
+RAKKTKSRKGQNNNKEGAAAPQAGEQAAGGAQAGGRKRQRAGKERTEEQKAEEAEKENRQTEKTRKAAR
+SAGPAKGRKTTRATRQPAQTDGANKQQKQEKTENTTTEETAEEGGEEKAKQNNRKTGDSGTPKKERGQA
+AGTGAGKTGEEPEGKKHGRQPGTKEGERRSKAQEEDKAEKDGEGGTGGQRARARAKADPGTEKEESKAN
+KTRTKEKKADKEGSSGTEQQPDSKGDQAERRTETHREGAPTETKKQKQTGEGEKRKPNRKQKTPQGEEE
+PERRPEQGEAPRSSTGPTQARRRQNTHNQGQNHRKTTATRKAPQANTERRQETGEEENEEDKEESPATT
+NTRTHKSAEAAGNTPQDKGTRNSATSTGADTAGRGPTTKHHKQAPTNTKAGGRKADPTDQGAAAQPATP
+ARAQTQQKQEEGRPTTSKGTRAGRQPETHKATANTRQREATTTGEGEGRGTATQANSSRSRKDPTEGKP
+TKTKPKGQKEHKKDPGGQTKTAKTEGGAENPGQRGGRTGGKTARNTEGEQGTQQRKAGPQKGTRKNPEQ
+QEKAEGREQPGKDGGSGHKQARKAKEPAPTQRRTKQAATEHREAEQQEENKRQQKNERSRQASPDRKPH
+RNSKKKPQAAKEETEEEQTR
[download]

It is not at all clear to me why, and it is not at all related to CFTR. For that matter, it's not related to any protein in public databases. Congradulations, you did gene discovery; pharamceutical companies spent billions of dollars to do that :-) Also, japhy's code returns nothing (except some line feeds apparently).

So, can anyone point out the problems with these subs? I copied them directly from the html, and only removed "+" at the beginning of code wrapped lines, and changed the name of the subs. Here is my code:

#!/usr/bin/perl 

while (<DATA>) {
  $cftr=$_;
}

print "tadman original\n".f0($cftr)."\n\n";
print "japhy\n".f1($cftr)."\n\n";
print "MeowChow\n".f2($cftr)."\n\n";
print "no_slogan\n".f3($cftr)."\n\n";
print "srawls\n".f4($cftr)."\n\n";
print "tachyon\n".RNA($cftr)."\n\n";
print "tadman golf\n".f5($cftr)."\n\n";

sub f0 {  # orginal by tadman
my %g = (
        # . - Stop
        'UAA'=>'.','UAG'=>'.','UGA'=>'.',
        # A - Alanine
        'GCU'=>'A','GCC'=>'A','GCA'=>'A','GCG'=>'A',
        # C - Cysteine
        'UGU'=>'C','UGC'=>'C',
        # D - Aspartic Acid
        'GAU'=>'D','GAC'=>'D',
        # E - Glutamic Acid
        'GAA'=>'E','GAG'=>'E',
        # F - Phenylalanine
        'UUU'=>'F','UUC'=>'F',
        # G - Glycine
        'GGU'=>'G','GGC'=>'G','GGA'=>'G','GGG'=>'G',
        # H - Histidine
        'CAU'=>'H','CAC'=>'H',
        # I - Isoleucine
        'AUU'=>'I','AUC'=>'I','AUA'=>'I',
        # K - Lysine
        'AAA'=>'K','AAG'=>'K',
        # L - Leucine
        'CUU'=>'L','CUC'=>'L','CUA'=>'L','CUG'=>'L',
        'UUA'=>'L','UUG'=>'L',
        # M - Methionine
        'AUG'=>'M',
        # N - Asparagine
        'AAU'=>'N','AAC'=>'N',
        # P - Proline
        'CCU'=>'P','CCC'=>'P','CCA'=>'P','CCG'=>'P',
        # Q - Glutamine
        'CAA'=>'Q','CAG'=>'Q',
        # R - Arginine
        'CGU'=>'R','CGC'=>'R','CGA'=>'R','CGG'=>'R',
        'AGA'=>'R','AGG'=>'R',
        # S - Serine
        'UCU'=>'S','UCC'=>'S','UCA'=>'S','UCG'=>'S',
        'AGU'=>'S','AGC'=>'S',
        # T - Threonine
        'ACU'=>'T','ACC'=>'T','ACA'=>'T','ACG'=>'T',
        # V - Valine
        'GUU'=>'V','GUC'=>'V','GUA'=>'V','GUG'=>'V',
        # W - Tryptophan
        'UGG'=>'W',
        # Y - Tyrosine
        'UAU'=>'Y','UAC'=>'Y',
);
$_=pop;s/.{1,3}/$g{$&}/g;$_
}


sub     #japhy
        B(){''}sub
        Z(){(B)x13}sub
        U(){(B)x31}sub
        O(){(B)x83}sub
        J(){(B)x343}sub
        b(){B,B,B}@g{AAA..UUU}=(K,B,N,b,K,Z,N,U,T,B,T,b,T,Z,T,O,R,B,S,
+b,R,Z,S,J,
        I,B,I,b,M,Z,I,(B)x811,Q,B,H,b,Q,Z,H,U,P,B,P,b,P,Z,P,O,R,B,R,b,
+R,Z,R,J,L,
        B,L,b,L,Z,L,(B)x2163,E,B,D,b,E,Z,D,U,A,B,A,b,A,Z,A,O,G,B,G,b,G
+,Z,G,J,V,B
        ,V,b,V,Z,V,(B)x8923,'.',B,Y,b,'.',Z,Y,U,S,B,S,b,S,Z,S,O,'.',B,
+C,b,W,Z,C,
        J,L,B,F,b,L,Z,F);sub
        f1{$_=pop;s/..?.?/$g{$&}/g;$_}

sub f2{ #MeowChow
my@r=qw(UA[AG]|UGA GC. - UG[UC] GA[UC] GA[AG] UU[UC] GG. CA[UC] AU[^G]
+ - AA[AG] CU.|UU[AG] AUG AA[UC] - CC. CA[AG] CG.|AG[AG] UC.|AG[UC] AC
+. - GU. UGG - UA[UC] ^);
((my$t=pop)=~s|..?.?|chr 64+(grep$&=~/$r[$_]/,0..26)[0]|eg);$t=~y/@Z/.
+/d;$t
}

sub f3 { #no_slogan
$_="KNNKtIIIMRSSRQHHQplr.YY.sLFFL.CCWEDDEavg";s/[a-z]/uc$&x4/eg;@x=/./
+g;join"",@x[map{$x=0;$x=$x*4|6&ord for/./g;$x/2}pop=~/.../g]
}

sub f4 {  #srawls
$_="KNNKtIIIMRSSRQHHQplr.YY.sLFFL.CCWEDDEavg";s/[a-z]/uc$&x4/eg;
join"",(/./g)[map{$x=0;$x=$x*4|6&ord for/./g;$x/2}pop=~/.../g] 
}

sub RNA { #tachyon
@_{'UAAUAGUGAGCUGCCGCAGCGUGUUGCGAUGACGAAGAGUUUUUCGGUGGCGGAGGGCAUCACAUU
+AUCAUAAAAAAGCUUCUCCUACUGUUAUUGAUGAAUAACCCUCCCCCACCGCAACAGCGUCGCCGACGG
+AGAAGG
UCUUCCUCAUCGAGUAGCACUACCACAACGGUUGUCGUAGUGUGGUAUUAC'=~/(...)/g}=split/
+/,'...AAAACCDDEEFFGGGGHHIIIKKLLLLLLMNNPPPPQQRRRRRRSSSSSSTTTTVVVVWYY';
+$_=pop
;s/..?.?/$_{$&}/g;$_
}

sub f5{  #tadman
$_=pop;y/UCAG/0123/;s/(.)(.)(.)/substr
"FFLLSSSSYY..CC.WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG"
,$1<<4|$2<<2|$3,1/ge;y/0123//d;$_
}

#>gi|6995995|ref|NM_000492.2| Homo sapiens cystic fibrosis transmembra
+ne conductance regulator, ATP-binding cassette (sub-family C, member 
+7) (CF
TR), mRNA
__DATA__
AUGCAGAGGUCGCCUCUGGAAAAGGCCAGCGUUGUCUCCAAACUUUUUUUCAGCUGGACCAGACCAAUUU
+UGAGGAAAGGAUACAGACAGCGCCUGGAAUUGUCAGACAUAUACCAAAUCCCUUCUGUUGAUUCUGCUG
+ACAAUCUAUCUGAAAAAUUGGAAAGAGAAUGGGAUAGAGAGCUGGCUUCAAAGAAAAAUCCUAAACUCA
+UUAAUGCCCUUCGGCGAUGUUUUUUCUGGAGAUUUAUGUUCUAUGGAAUCUUUUUAUAUUUAGGGGAAG
+UCACCAAAGCAGUACAGCCUCUCUUACUGGGAAGAAUCAUAGCUUCCUAUGACCCGGAUAACAAGGAGG
+AACGCUCUAUCGCGAUUUAUCUAGGCAUAGGCUUAUGCCUUCUCUUUAUUGUGAGGACACUGCUCCUAC
+ACCCAGCCAUUUUUGGCCUUCAUCACAUUGGAAUGCAGAUGAGAAUAGCUAUGUUUAGUUUGAUUUAUA
+AGAAGACUUUAAAGCUGUCAAGCCGUGUUCUAGAUAAAAUAAGUAUUGGACAACUUGUUAGUCUCCUUU
+CCAACAACCUGAACAAAUUUGAUGAAGGACUUGCAUUGGCACAUUUCGUGUGGAUCGCUCCUUUGCAAG
+UGGCACUCCUCAUGGGGCUAAUCUGGGAGUUGUUACAGGCGUCUGCCUUCUGUGGACUUGGUUUCCUGA
+UAGUCCUUGCCCUUUUUCAGGCUGGGCUAGGGAGAAUGAUGAUGAAGUACAGAGAUCAGAGAGCUGGGA
+AGAUCAGUGAAAGACUUGUGAUUACCUCAGAAAUGAUUGAAAAUAUCCAAUCUGUUAAGGCAUACUGCU
+GGGAAGAAGCAAUGGAAAAAAUGAUUGAAAACUUAAGACAAACAGAACUGAAACUGACUCGGAAGGCAG
+CCUAUGUGAGAUACUUCAAUAGCUCAGCCUUCUUCUUCUCAGGGUUCUUUGUGGUGUUUUUAUCUGUGC
+UUCCCUAUGCACUAAUCAAAGGAAUCAUCCUCCGGAAAAUAUUCACCACCAUCUCAUUCUGCAUUGUUC
+UGCGCAUGGCGGUCACUCGGCAAUUUCCCUGGGCUGUACAAACAUGGUAUGACUCUCUUGGAGCAAUAA
+ACAAAAUACAGGAUUUCUUACAAAAGCAAGAAUAUAAGACAUUGGAAUAUAACUUAACGACUACAGAAG
+UAGUGAUGGAGAAUGUAACAGCCUUCUGGGAGGAGGGAUUUGGGGAAUUAUUUGAGAAAGCAAAACAAA
+ACAAUAACAAUAGAAAAACUUCUAAUGGUGAUGACAGCCUCUUCUUCAGUAAUUUCUCACUUCUUGGUA
+CUCCUGUCCUGAAAGAUAUUAAUUUCAAGAUAGAAAGAGGACAGUUGUUGGCGGUUGCUGGAUCCACUG
+GAGCAGGCAAGACUUCACUUCUAAUGAUGAUUAUGGGAGAACUGGAGCCUUCAGAGGGUAAAAUUAAGC
+ACAGUGGAAGAAUUUCAUUCUGUUCUCAGUUUUCCUGGAUUAUGCCUGGCACCAUUAAAGAAAAUAUCA
+UCUUUGGUGUUUCCUAUGAUGAAUAUAGAUACAGAAGCGUCAUCAAAGCAUGCCAACUAGAAGAGGACA
+UCUCCAAGUUUGCAGAGAAAGACAAUAUAGUUCUUGGAGAAGGUGGAAUCACACUGAGUGGAGGUCAAC
+GAGCAAGAAUUUCUUUAGCAAGAGCAGUAUACAAAGAUGCUGAUUUGUAUUUAUUAGACUCUCCUUUUG
+GAUACCUAGAUGUUUUAACAGAAAAAGAAAUAUUUGAAAGCUGUGUCUGUAAACUGAUGGCUAACAAAA
+CUAGGAUUUUGGUCACUUCUAAAAUGGAACAUUUAAAGAAAGCUGACAAAAUAUUAAUUUUGAAUGAAG
+GUAGCAGCUAUUUUUAUGGGACAUUUUCAGAACUCCAAAAUCUACAGCCAGACUUUAGCUCAAAACUCA
+UGGGAUGUGAUUCUUUCGACCAAUUUAGUGCAGAAAGAAGAAAUUCAAUCCUAACUGAGACCUUACACC
+GUUUCUCAUUAGAAGGAGAUGCUCCUGUCUCCUGGACAGAAACAAAAAAACAAUCUUUUAAACAGACUG
+GAGAGUUUGGGGAAAAAAGGAAGAAUUCUAUUCUCAAUCCAAUCAACUCUAUACGAAAAUUUUCCAUUG
+UGCAAAAGACUCCCUUACAAAUGAAUGGCAUCGAAGAGGAUUCUGAUGAGCCUUUAGAGAGAAGGCUGU
+CCUUAGUACCAGAUUCUGAGCAGGGAGAGGCGAUACUGCCUCGCAUCAGCGUGAUCAGCACUGGCCCCA
+CGCUUCAGGCACGAAGGAGGCAGUCUGUCCUGAACCUGAUGACACACUCAGUUAACCAAGGUCAGAACA
+UUCACCGAAAGACAACAGCAUCCACACGAAAAGUGUCACUGGCCCCUCAGGCAAACUUGACUGAACUGG
+AUAUAUAUUCAAGAAGGUUAUCUCAAGAAACUGGCUUGGAAAUAAGUGAAGAAAUUAACGAAGAAGACU
+UAAAGGAGUGCCUUUUUGAUGAUAUGGAGAGCAUACCAGCAGUGACUACAUGGAACACAUACCUUCGAU
+AUAUUACUGUCCACAAGAGCUUAAUUUUUGUGCUAAUUUGGUGCUUAGUAAUUUUUCUGGCAGAGGUGG
+CUGCUUCUUUGGUUGUGCUGUGGCUCCUUGGAAACACUCCUCUUCAAGACAAAGGGAAUAGUACUCAUA
+GUAGAAAUAACAGCUAUGCAGUGAUUAUCACCAGCACCAGUUCGUAUUAUGUGUUUUACAUUUACGUGG
+GAGUAGCCGACACUUUGCUUGCUAUGGGAUUCUUCAGAGGUCUACCACUGGUGCAUACUCUAAUCACAG
+UGUCGAAAAUUUUACACCACAAAAUGUUACAUUCUGUUCUUCAAGCACCUAUGUCAACCCUCAACACGU
+UGAAAGCAGGUGGGAUUCUUAAUAGAUUCUCCAAAGAUAUAGCAAUUUUGGAUGACCUUCUGCCUCUUA
+CCAUAUUUGACUUCAUCCAGUUGUUAUUAAUUGUGAUUGGAGCUAUAGCAGUUGUCGCAGUUUUACAAC
+CCUACAUCUUUGUUGCAACAGUGCCAGUGAUAGUGGCUUUUAUUAUGUUGAGAGCAUAUUUCCUCCAAA
+CCUCACAGCAACUCAAACAACUGGAAUCUGAAGGCAGGAGUCCAAUUUUCACUCAUCUUGUUACAAGCU
+UAAAAGGACUAUGGACACUUCGUGCCUUCGGACGGCAGCCUUACUUUGAAACUCUGUUCCACAAAGCUC
+UGAAUUUACAUACUGCCAACUGGUUCUUGUACCUGUCAACACUGCGCUGGUUCCAAAUGAGAAUAGAAA
+UGAUUUUUGUCAUCUUCUUCAUUGCUGUUACCUUCAUUUCCAUUUUAACAACAGGAGAAGGAGAAGGAA
+GAGUUGGUAUUAUCCUGACUUUAGCCAUGAAUAUCAUGAGUACAUUGCAGUGGGCUGUAAACUCCAGCA
+UAGAUGUGGAUAGCUUGAUGCGAUCUGUGAGCCGAGUCUUUAAGUUCAUUGACAUGCCAACAGAAGGUA
+AACCUACCAAGUCAACCAAACCAUACAAGAAUGGCCAACUCUCGAAAGUUAUGAUUAUUGAGAAUUCAC
+ACGUGAAGAAAGAUGACAUCUGGCCCUCAGGGGGCCAAAUGACUGUCAAAGAUCUCACAGCAAAAUACA
+CAGAAGGUGGAAAUGCCAUAUUAGAGAACAUUUCCUUCUCAAUAAGUCCUGGCCAGAGGGUGGGCCUCU
+UGGGAAGAACUGGAUCAGGGAAGAGUACUUUGUUAUCAGCUUUUUUGAGACUACUGAACACUGAAGGAG
+AAAUCCAGAUCGAUGGUGUGUCUUGGGAUUCAAUAACUUUGCAACAGUGGAGGAAAGCCUUUGGAGUGA
+UACCACAGAAAGUAUUUAUUUUUUCUGGAACAUUUAGAAAAAACUUGGAUCCCUAUGAACAGUGGAGUG
+AUCAAGAAAUAUGGAAAGUUGCAGAUGAGGUUGGGCUCAGAUCUGUGAUAGAACAGUUUCCUGGGAAGC
+UUGACUUUGUCCUUGUGGAUGGGGGCUGUGUCCUAAGCCAUGGCCACAAGCAGUUGAUGUGCUUGGCUA
+GAUCUGUUCUCAGUAAGGCGAAGAUCUUGCUGCUUGAUGAACCCAGUGCUCAUUUGGAUCCAGUAACAU
+ACCAAAUAAUUAGAAGAACUCUAAAACAAGCAUUUGCUGAUUGCACAGUAAUUCUCUGUGAACACAGGA
+UAGAAGCAAUGCUGGAAUGCCAACAAUUUUUGGUCAUAGAAGAGAACAAAGUGCGGCAGUACGAUUCCA
+UCCAGAAACUGCUGAACGAGAGGAGCCUCUUCCGGCAAGCCAUCAGCCCCUCCGACAGGGUGAAGCUCU
+UUCCCCACCGGAACUCAAGCAAGUGCAAGUCUAAGCCCCAGAUUGCUGCUCUGAAAGAGGAGACAGAAG
+AAGAGGUGCAAGAUACAAGGCUUUAG
[download]

Happy debugging golfed code,
Scott