Word of advice, pick "for" or "foreach" and use one. Minor nit, but they're interchangable, and switching back and forth tends to make it less readable for me.

And just a quick note: 

for( my $i=1; $i<@aas; $i++){
   #etc
}

[download]
can be written more perlish as (assuming you really want elements 0 .. $#aas of @aas, instead of 1..$#aas+1): 
for( @aas ){
  @codons = @{$Deg_codons{$_}};
  for my $seq( keys %SEQ ){
    for my $codon( @codons ){
      $SEQ{$seq.$codon}=1; 
    }
    delete $SEQ{$seq};
  }
}

[download]

There are probably some other changes that could be made here, but these are just the ones that jump off the page at me.



--chargrill 
$,=42;for(34,0,-3,9,-11,11,-17,7,-5){$*.=pack'c'=>$,+=$_}for(reverse s
+plit//=>$*
){$%++?$ %%2?push@C,$_,$":push@c,$_,$":(push@C,$_,$")&&push@c,$"}$C[$#
+C]=$/;($#C
>$#c)?($ c=\@C)&&($ C=\@c):($ c=\@c)&&($C=\@C);$%=$|;for(@$c){print$_^
+$$C[$%++]}

[download]

In reply to Re: foreach to for by chargrill
in thread foreach to for by tricolaire

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