[Bioperl-l] K-mer generating script

[Mark A. Jensen]

A little sloppy, but it recurses and is general---

# ex...
@combs = doit(3, [ qw( A T G C ) ]);
1;
# code

sub doit {
    my ($n, $sym) = @_;
    my $a = [];
    doit_guts($n, $sym, $a, '');
    return map {$_ || ()} @$a;
}

sub doit_guts {
  my ($n, $sym, $store, $str)  = @_;
  if (!$n) {
    return $str;
  }
  else {
    foreach my $s (@$sym) {
      push @$store, doit_guts($n-1, $sym, $store, $str.$s);
    }
  }
}


----- Original Message ----- 
From: "Blanchette, Marco" <MAB at stowers-institute.org>
To: <bioperl-l at lists.open-bio.org>
Sent: Friday, December 19, 2008 6:25 PM
Subject: [Bioperl-l] K-mer generating script


> Dear all,
>
> Does anyone have a little function that I could use to generate all possible 
> k-mer DNA sequences? For instance all possible 3-mer (AAA, AAT, AAC, AAG, 
> etc...). I need something that I could input the value of k and get all 
> possible sequences...
>
> I know that it's a problem that need to use recursive programming but I can't 
> get my brain around the problem.
>
> Many thanks
>
> Marco
> --
> Marco Blanchette, Ph.D.
> Assistant Investigator
> Stowers Institute for Medical Research
> 1000 East 50th St.
>
> Kansas City, MO 64110
>
> Tel: 816-926-4071
> Cell: 816-726-8419
> Fax: 816-926-2018
>
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>
>