[Bioperl-l] K-mer generating script

Mon Jan 5 21:44:23 UTC 2009

Malcolm, Russell-- excellent! MAJ
----- Original Message ----- 
From: "Smithies, Russell" <Russell.Smithies at agresearch.co.nz>
To: "'bioperl list'" <bioperl-l at lists.open-bio.org>
Sent: Monday, January 05, 2009 3:43 PM
Subject: Re: [Bioperl-l] K-mer generating script


> Yet another way with recursive use of map:
>
> print "[", join(", ", @$_), "]\n" for
> permute([ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G C ) ],[ qw( A T G 
> C ) ]);
>
> sub permute {
>  my $last = pop @_;
>  unless (@_) {
>    return map [$_], @$last;
>  }
>  return map { my $left = $_; map [@$left, $_], @$last } permute(@_);
> }
>
>
> (Modified from a PerlMonks example http://perlmonks.org/?node_id=24270)
>
>
>> -----Original Message-----
>> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
>> bounces at lists.open-bio.org] On Behalf Of Cook, Malcolm
>> Sent: Tuesday, 6 January 2009 8:15 a.m.
>> To: 'Chris Fields'; 'Jason Stajich'
>> Cc: 'bioperl list'; 'Mark A. Jensen'; Blanchette, Marco
>> Subject: Re: [Bioperl-l] K-mer generating script
>>
>> Gang,
>>
>> I couldn't resist adding the following non-perl solution...
>>
>> #!/bin/bash
>> k=$1
>> s=$( printf "%${k}s" ); # a string with $k blanks
>> s=${s// /{A,T,G,C\}};   # substitute '{A,T,G,C}' for each of the k
>> blanks
>> echo 'kmers using bash to expand:' $s > /dev/stderr
>> bash -c "echo  $s";     # let brace expanion of inferior bash compute
>> the cross product
>>
>> -- Malcolm
>>
>>
>> > -----Original Message-----
>> > From: bioperl-l-bounces at lists.open-bio.org
>> > [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of
>> > Chris Fields
>> > Sent: Friday, December 19, 2008 11:54 PM
>> > To: Jason Stajich
>> > Cc: bioperl list; Mark A. Jensen; Blanchette, Marco
>> > Subject: Re: [Bioperl-l] K-mer generating script
>> >
>> > To add to the pile:
>> >
>> > Mark-Jason Dominus tackles this problem in Higher-Order Perl
>> > using iterators, which also allows other nifty bits like
>> > 'give variants of A(CTG)T(TGA)', where anything in
>> > parentheses are wild-cards.  The nice advantage of the
>> > iterator approach is you don't tank memory for long strings.
>> > Furthermore, as a bonus, you can now download the book for
>> > free:
>> >
>> > http://hop.perl.plover.com/book/
>> >
>> > The relevant chapter is here (p. 135):
>> >
>> > http://hop.perl.plover.com/book/pdf/04Iterators.pdf
>> >
>> > chris
>> >
>> > On Dec 19, 2008, at 11:02 PM, Jason Stajich wrote:
>> >
>> > > Does someone want to put this on the wiki too?
>> > >
>> > > Maybe we could start a little bit of perl snippets for
>> > examples like
>> > > these.
>> > >
>> > > -j
>> > > On Dec 19, 2008, at 7:45 PM, Mark A. Jensen wrote:
>> > >
>> > >> A little sloppy, but it recurses and is general---
>> > >>
>> > >> # ex...
>> > >> @combs = doit(3, [ qw( A T G C ) ]);
>> > >> 1;
>> > >> # code
>> > >>
>> > >> sub doit {
>> > >>  my ($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
>> > >>>
>> > >>
>> > >> _______________________________________________
>> > >> Bioperl-l mailing list
>> > >> Bioperl-l at lists.open-bio.org
>> > >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> > >
>> > > Jason Stajich
>> > > jason at bioperl.org
>> > >
>> > >
>> > >
>> > > _______________________________________________
>> > > Bioperl-l mailing list
>> > > Bioperl-l at lists.open-bio.org
>> > > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>> > _______________________________________________
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>> > Bioperl-l at lists.open-bio.org
>> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
>> >
>>
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