Re: Generate all possibilities

Jeff and larryk,
Thanks for your suggestions.
Jeff, I had already checked out your suggestions but they didn't cut the mustard. I probably wasn't specific enough in my original question but I need all the possibilities not the permutations (I'm not sure if that is the correct usage of possibilities/permutations . . .). Specifically I also need to generate sequences containing all the same base e.g. AAA, TTT etc.

The Ordered Combinations solution as suggested by larryk does what I need, an awesome little piece of code. Thanks to MeowChow, sachmet and tilly.

Here is the final piece of code for the record:

use strict;
#generate all posibilites of a DNA sequence
my @Bases = qw(A C G T);
my $SequenceMinLenght = 1;
my $SequenceMaxLength = 3;
my @SequenceLenghts = ($SequenceMinLenght...$SequenceMaxLength);
#print "@SequenceLenghts\n";
my $SequenceListLength = $#SequenceLenghts;
$SequenceListLength ++;
print "Number of Sequence lenghts to permute is $SequenceListLength\n"
+;
my @allSequence = ();
my $sequence;
my $currLenght;
my @Ordered_Combinations_input = ();
foreach $currLenght (@SequenceLenghts){
    @Ordered_Combinations_input = ();
    @Ordered_Combinations_input = ($currLenght, @Bases);
    @allSequence = (@allSequence, (&Ordered_Combinations (@Ordered_Com
+binations_input)));    
}
#Prints sequences to screen
# - Too many entries after lenght of sequence is grater than 4.  
my $i=0;
foreach my $finalsequence (@allSequence){
    $i ++;
    if ($i == 4){
        print "$finalsequence\n";
        $i= 0;
    }
    else{
        print "$finalsequence\t";
    }
}
#Completely blow the GOLF chalange by using a sub name almost as long 
+as the sub
#See http://www.perlmonks.com/index.pl?node_id=75261 for details 
sub Ordered_Combinations {my$n=shift;--$n?map{my$d=$_;map$d.$_,Ordered
+_Combinations($n,@_)}@_:@_};
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Re: Re: Generate all possibilities by CharlesClarkson (Curate) on Jun 21, 2001 at 12:05 UTC
Unless you need some of those variables later, we could eliminate some clutter. use strict; use warnings; #generate all posibilites of a DNA sequence my @Bases = qw(A C G T); my $SequenceMinLength = 1; my $SequenceMaxLength = 3; print 'Number of Sequence lengths to permute is ', $SequenceMaxLength - $SequenceMinLength + 1, "\n"; my @allSequence; foreach my $currLength ($SequenceMinLength .. $SequenceMaxLength){ push @allSequence, Ordered_Combinations($currLength, @Bases); } #Prints sequences to screen # - Too many entries after length of sequence is greater than 4. my $i; foreach my $finalsequence (@allSequence){ ++$i % @Bases ? print "$finalsequence\t" : print "$finalsequence\n +"; } [download] By using @Bases instead of 4, we get @Base columns, aiding readability. `sub Ordered_Combinations { my $n = shift; --$n ? map { my $d = $_; map "$d$_", Ordered_Combinations($n,@_) } @_ : @_ }` [download] HTH, Charles K. Clarkson	[reply] [d/l] [select]

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Re: Re: Generate all possibilities
by CharlesClarkson (Curate) on Jun 21, 2001 at 12:05 UTC

Unless you need some of those variables later, we could eliminate some clutter.

use strict;
use warnings;

#generate all posibilites of a DNA sequence
my @Bases = qw(A C G T);
my $SequenceMinLength = 1;
my $SequenceMaxLength = 3;
print 'Number of Sequence lengths to permute is ',
      $SequenceMaxLength - $SequenceMinLength + 1, "\n";

my @allSequence;
foreach my $currLength ($SequenceMinLength .. $SequenceMaxLength){
    push @allSequence, Ordered_Combinations($currLength, @Bases);
}

#Prints sequences to screen
# - Too many entries after length of sequence is greater than 4.
my $i;
foreach my $finalsequence (@allSequence){
    ++$i % @Bases ? print "$finalsequence\t" : print "$finalsequence\n
+";
}
[download]

By using @Bases instead of 4, we get @Base columns, aiding readability.

sub Ordered_Combinations {
    my $n = shift;
    --$n ? map {
             my $d = $_;
             map "$d$_", Ordered_Combinations($n,@_)
               } @_
         : @_
}
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