[Bioperl-l] K-mer generating script

[Smithies, Russell]

Aaarrgg, it's starting to look like some bastard child of Python and Haskell!!!

;-)

> -----Original Message-----
> From: Chris Fields [mailto:cjfields at illinois.edu]
> Sent: Tuesday, 6 January 2009 10:46 a.m.
> To: Smithies, Russell
> Cc: 'bioperl list'
> Subject: Re: [Bioperl-l] K-mer generating script
> 
> Perl 6 (20 random 20-mers):
> 
> use v6;
> 
> say [~] <A T G C>.pick(20, :repl) for 1..20;
> 
> -chris
> 
> On Jan 5, 2009, at 2:43 PM, Smithies, Russell wrote:
> 
> > 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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> >>>
> >>
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