[Bioperl-l] K-mer generating script

[Jason Stajich]

Does someone want to put this on the wiki too?

Maybe we could start a little bit of perl snippets for examples like  
these.

-j
On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote:

> 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
>>
>> _______________________________________________
>> Bioperl-l mailing list
>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>
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Jason Stajich
jason at bioperl.org