Re: string complement question

Mmmm, my bad. I wasn't paying much attention (apparantly). I was still checking and printing the same stuff, which didn't really make sense. This should do the trick (still slow, and I'm looking forward to faster ways :)

my $i;
my $j;
my $dna;
my $temp_dna;

for ($i=0; $i < @array1; $i++) {
   $dna = $array1[$i];
   $temp_dna = $dna;
   $dna = reverse $dna;
   $dna =~ tr/actg/tgac/;

   for ($j=0; $j < @array1; $j++) {
      if ($dna eq $array1[$j]) {
         print "FOUND $temp_dna\t$array[$j]\n";
      }
   }
}
[download]

Please note that I made a lot of steps to get to this. This could be shortened, but this is more readable (for me at least ;)

--
B10m

Comment on Re: string complement question Download Code

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Re: string complement question by Abigail-II (Bishop) on Nov 21, 2003 at 13:55 UTC
Well, if it's just finding matches inside the same array, it's just a variation on finding uniques in an array. Here's one way of solving it: #!/usr/bin/perl use strict; use warnings; my @array = qw /TATG GTTC GAAC AATA/; # DNA's tend to be loooooooooooooooong, so we create a lookup # table to calculate the reversed inverse. my %table; my @chars = qw /A C G T/; foreach my $c1 (@chars) { foreach my $c2 (@chars) { foreach my $c3 (@chars) { foreach my $c4 (@chars) { my $val = reverse my $key = "$c1$c2$c3$c4"; $val =~ y/ACGT/TGCA/; $table {$key} = $val; } } } } my %tmp; @tmp {@array} = (); my @matches = grep {exists $tmp {$table {$_}}} @array; print "@matches\n"; __END__ [download] Abigail	[reply] [d/l]

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Re: string complement question
by Abigail-II (Bishop) on Nov 21, 2003 at 13:55 UTC

#!/usr/bin/perl

use strict;
use warnings;

my @array = qw /TATG GTTC GAAC AATA/;
        
# DNA's tend to be loooooooooooooooong, so we create a lookup
# table to calculate the reversed inverse.
my %table;
my @chars = qw /A C G T/;
foreach my $c1 (@chars) {
    foreach my $c2 (@chars) {
        foreach my $c3 (@chars) {
            foreach my $c4 (@chars) {
                my $val = reverse my $key = "$c1$c2$c3$c4";
                   $val =~ y/ACGT/TGCA/;
                $table {$key} = $val;
            }
        }
    }
}

my %tmp; @tmp {@array} = ();
my @matches = grep {exists $tmp {$table {$_}}} @array;

print "@matches\n";

__END__
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Abigail

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