my %ref;
my $threelinefakein = "...\n...";
fillRef( \%ref, \$threelinefakein );

my @fakes = ( "1\n2\n3", "1\n2\n3" );
for my $fake ( @fakes ){

   refLogic( \%ref, \$fake );
}

##</code><code>##

## Usage: fillRef( $hashref, $infilename );
sub fillRef {
## so you can keep using $ref{blah}
## less rewriting when you copy/paste
   local *ref = shift;
## open the string as file
   open IN, '<', shift;
   ...
}


## Usage: refLogic( $hashref, $infilename );
sub refLogic {
   local *ref = shift;
## open the string as file
   open IN, '<', shift;
## fake out for testing
   local *OUT = \*STDOUT;
}
##</code><code>##

    my %ref    = ... ; ## Data::Dump::dd(%ref)    output here
    my @probes = ... ; ## Data::Dump::dd(@probes) output here
##
    foreach my $key ( sort keys %ref ) {

        #intended function
        print OUT $ref{$key} . "\t" . $probes[$key];

        #testing
        my @temp = split "\t", $ref{$key};
        foreach (@temp) {
            if ( $temp[0] == 2 ) {
                print $key. "\t" . $ref{$key} . "\t" . $probes[$key];
            }
        }
    }
##
    foreach my $key ( sort keys %ref ) {
        print OUT $ref{$key} . "\t" . $probes[$key];
        my @temp = split "\t", $ref{$key};
        foreach (@temp) {
            if ( $temp[0] == 2 ) { print $key. "\t" . $ref{$key} . "\n"; }
        }
    }