I made a few minor adjustments:

die "cannot open ${infile1}: $!\n" unless open $IN1, '<', $infile1;
die "cannot open ${infile2}: $!\n" unless open $IN2, '<', $infile2;
die "cannot open ${outfile}: $!\n" unless open $OUT, '>', $outfile;

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}
                    and $UR_CI{$value1} ne $CI_UR{$value2} )
                {
                    delete $UR_CI{$key1};
                }
            }
        }
    }
}
while ( my ( $key, $value ) = each %UR_CI ) {
    print $OUT "$key => $value\n";
}

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In reply to Re: Hash Comparisions by Khen1950fx
in thread Hash Comparisions by perl_n00b

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