in reply to Trying to construct all possible strings from 4 bases [ATCG]

this seemes to be a case for recursive programming. if i understood you correctly, this code should do what you want.
#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $l = 2;    #Motif Length
my @nucs = qw/A T C G/;

my @enum = enum( $l, \@nucs );
print Dumper \@enum;

sub enum {
    return @{$_[1]} unless --$_[0];
    map { my $nuc = $_; map { $nuc . $_ } @{$_[1]} } enum( $_[0], $_[1
+]);
}

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Re^2: Trying to construct all possible strings from 4 bases [ATCG]
by monkfan (Curate) on Feb 21, 2005 at 11:24 UTC
    Hi Taumaril,
    Thanks so much for answering me.

    Using recursive along with map is way tooooo.. high for me.
    Would you mind explain it with "for" loop instead?

    As I don't have a strong background algorithmic way of thinking,
    I would like to understand recursion in more basic way.
    I hope this is not too much to ask ;-)

    Regards,
    Edward
[reply]
      hi,
      it's not too mutch to ask. in fact i'm relay glad to explain some code, 'cause it shows, that you are willing to learn. so here it comes:

      ### my recursive subroutine
###########################
sub enum {

    ### return the list of elements (aka nucleotides) if this is the l
+ast
    ### recursion.
    ### also note that --$_[0] decrements the counter _before_ it is t
+ested
    ##################################################################
+#####
    return @{$_[1]} unless --$_[0];

    ### define a variable which holds my return values
    ##################################################
    my @return;

    ### iterate over the return values of the next recursion
    ########################################################
    for ( enum( $_[0], $_[1] ) ){
        my $nuc = $_;

        ### iterate over all nucleotides
        ################################
        for ( @{$_[1]} ) {
            push @return, $nuc . $_;
        }
    }

    ### return the list so far to the prior recursion
    #################################################
    return @return;
}

      [download]

      if you have problems to understand how it works, try to think about what happens, when $_[0] = 1 then think about what happens, when $_[0] = 2 and then you should get it.
      if you don't understand this at all, it could be because my english is not even close to perfect. so maybe i just didn't explain it correct, which means "don't hesitate to ask questions" :-)
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