use warnings;
use strict;


my %bow1 = ();
my $file1 = shift;
open (FILE1, "$file1"); # Open first file

while (<FILE1>) {
	my ($ID1, undef, undef, undef, $Seq1) = split;
	$bow1{$ID1} = $ID1;
	$bow1{$Seq1} = $Seq1;
	print STDERR "$bow1{$ID1}\t$bow1{$Seq1}\n";
}
close FILE1;


my %bow2 = ();
my $file2 = shift;

open (FILE2, "$file2"); # Open second file

while (<FILE2>) {
    my ($ID2, undef, undef, undef, $Seq2) = split;
	$bow2{$ID2} = $ID2;
	$bow2{$Seq2} = $Seq2;
	print STDERR "$bow2{$ID2}\t$bow2{$Seq2}\n";
}
close FILE2;

foreach my $ID1 (keys %bow1){ # can use (sort keys %hash) to put items in a specified order
   if ( exists $bow2{$ID2} ){
      if ( $bow1{$ID1} eq $bow2{$ID2} ){
         ## id and sequence are stored as key value pairs
         print "$bow1{$ID1} exists in $file1 and $file2 and the sequences match $bow1{$Seq1} $bow2{$Seq2} \n";
      }
      else{
		print "$bow1{$ID1} exists in $file1 and $file2 but sequences DO NOT match $bow1{$Seq1} $bow2{$Seq2} \n";
      }
   }
   else {
      print "$bow1{$ID1} only exists in $file1 .\n";
}

}



exit;

##</code><code>##

Global symbol "$ID2" requires explicit package name at /home/choia2/scripts/BowtieCompare.pl line 50.
Global symbol "$ID2" requires explicit package name at /home/choia2/scripts/BowtieCompare.pl line 51.
Global symbol "$Seq1" requires explicit package name at /home/choia2/scripts/BowtieCompare.pl line 53.
Global symbol "$Seq2" requires explicit package name at /home/choia2/scripts/BowtieCompare.pl line 53.
Global symbol "$Seq1" requires explicit package name at /home/choia2/scripts/BowtieCompare.pl line 56.
Global symbol "$Seq2" requires explicit package name at /home/choia2/scripts/BowtieCompare.pl line 56.
Execution of /home/choia2/scripts/BowtieCompare.pl aborted due to compilation errors.