[Bioperl-l] Reverse Comp Coding Puzzler

[shawnh at fugu-sg.org]

Interesting..had a look around perlmonks.com, adopting a solution found here:
http://perlmonks.thepen.com/154008.html

 my @M = qw(ATG);
 my @P = qw(CCA CCC CCG CCT);
 my @V = qw(GTA GTC GTG GTT);
 my @A = qw(GCA GCC GCG GCT);
 my @R = qw(CGA CGC CGG CGT AGA AGG);
 my @D = qw(GAC GAT);
 my @I = qw(ATA ATC ATT);

my @aoa = ([(0)],[(0..3)],[(0..3)],[(0..3)],[(0..5)],[(0..1)],[(0..2)] );


my $iter = make_permutator(@aoa);
while (my ($m,$p,$v,$a,$r,$d,$i) = $iter->() ){
  print $M[$m].$P[$p].$V[$v].$A[$a].$R[$r].$D[$d].$I[$i]."\n";
}
sub make_permutator{
    my @arefs = @_;
    my @arrayindexes = ();
    foreach (@arefs){
        push @arrayindexes,[$_,0,$#{$_}];
    }
    return sub {
        return if $arrayindexes[0]->[1] > $arrayindexes[0]->[2];
        my @els =  map { $_->[0]->[ $_->[1]] } @arrayindexes;
        # Check for out of bounds....
         $arrayindexes[$#arrayindexes]->[1]++;
         for (my $i = $#arrayindexes; $i > 0; $i--){
             if ($arrayindexes[$i]->[1] > $arrayindexes[$i]->[2]){
                 $arrayindexes[$i]->[1] = 0;
                 $arrayindexes[$i-1]->[1]++;
                 }else{
                     last;
                 }
            }
            return @els;
   };
}
This might do the trick.
cheers,

shawn


On Mon, 13 Jan 2003, David Nix wrote:

> Hello Folks,
>     I'm working on a perl program that identifies all restriction sites that
> can be inserted or deleted from an oligo used for site directed mutagenesis
> without changing the encoded amino acid sequence.  One problem that I need
> to overcome is how to get all unique oligo permutations of a 7 amino acid
> peptide, preferably one at a time.  These will be restriction mapped,
> compared to the original sequence one is mutating, and any differences
> ranked and returned to the user.
> 
> At first pass this seems like it should be easy, I can do it with pencil and
> paper, but getting it into a perl script is proving challenging for my
> novice programming skills.  Any suggestions or pointers you would have would
> be greatly appreciated!
> 
> Here's an example:
> 
> Take a peptide like...
> 
>  M  P  V  A  R  D  I
> 
> Each amino acid is encoded by the following (I've got them in arrays)...
>  my @M = qw(ATG);
>  my @P = qw(CCA CCC CCG CCT);
>  my @V = qw(GTA GTC GTG GTT);
>  my @A = qw(GCA GCC GCG GCT);
>  my @R = qw(CGA CGC CGG CGT AGA AGG);
>  my @D = qw(GAC GAT);
>  my @I = qw(ATA ATC ATT);
> 
> A few oligo permutation would be...
> $oligo1 = $M[0] . $P[0] . $V[0] . $A[0] . $R[0] . $D[0] . $I[0];
> $oligo2 = $M[0] . $P[0] . $V[0] . $A[0] . $R[0] . $D[0] . $I[1];
> $oligo3 = $M[0] . $P[0] . $V[0] . $A[0] . $R[0] . $D[0] . $I[2];
> 
> Now how would one write a script that gets at all the other 2301
> permutations (1 x 4 x 4 x 4 x 6 x 2 x 3)!  Ugg!  I've been at this for a day
> without much luck!  Suggestions?
> 
> Cheers, 
> Dave
> 
> 

-- 
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************