Okay I have another one for you guys:
This code is extremely inefficient (edit: actually I don't think this even works and something in it is hanging my system). Is there a better way to write it? (my files are very large)
I have 2 files that look like this:
UR_CI file 
G_00160 F_02571
G_00161 F_01082
G_00162 F_00034
G_00163 F_00035
G_00164 F_00036

[download]
and
CI_UR file
F_00013 G_06670
F_00034 G_00162
F_00035 G_00163
F_00036 G_00164
F_00038 G_00165

[download]

I am trying to find the matches that look like "G_00163 F_00035" & "F_00035 G_00163" 
open $IN1, "<", $infile1 or die "cannot open $infile1: $!\n";
open $IN2, "<", $infile2 or die "cannot open $infile2: $!\n";
open $OUT, ">", $outfile or die "cannot open $outfile: $!\n";

my(@UR_CI) = <$IN1>;
my(@CI_UR) = <$IN2>;

my(%UR_CI, %CI_UR);

foreach my $seq (@UR_CI) {
   if ($seq =~ /^(\w+)\s+(\w+)$/) {
      $UR_CI{"$1"} = "$2";
   }
}

foreach my $seq (@CI_UR) {
   if ($seq =~ /^(\w+)\s+(\w+)$/) {
      $CI_UR{"$2"} = "$1";
   }
}

foreach my $key1 (keys %UR_CI) {
foreach my $key2 (keys %CI_UR) {
foreach my $value1 (values %UR_CI) {
foreach my $value2 (values %CI_UR) {
   if (($UR_CI{$key1} eq $CI_UR{$key2}) && ($UR_CI{$value1} ne $CI_UR{
+$value2})) {
         delete $UR_CI{$key1};
   }
}
}
}
}

while ( my ($key, $value) = each(%UR_CI) ) {
        print $OUT "$key => $value\n";
}

[download]

Any ideas?
Any help is greatly appreciated!

In reply to Hash Comparisions by perl_n00b

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