#!/usr/bin/perl
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}[0] = $ID1;
	$bow1{$ID1}[1] = $Seq1;
}
close FILE1;


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

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

while (<FILE2>) {
    my ($ID2, undef, undef, undef, $Seq2) = split;
	$bow2{$ID2}[0] = $ID2;
	$bow2{$ID2}[1] = $Seq2;
}
close FILE2;

for my $ID1 (keys %bow1) {
	for my $ID2 (keys %bow2) {
		if (defined $bow1{$ID1}[0] and defined $bow2{$ID2}[0]) {
			if ($bow1{$ID1}[0] eq $bow2{$ID2}[0]) {
				if ($bow1{$ID1}[1] =! $bow2{$ID2}[1] ) { 
					print "$bow1{$ID1}[0]\t$bow1{$ID1}[1]\t$bow2{$ID2}[0]\t$bow2{$ID2}[1]\n";
				}
			}
			if ($bow1{$ID1}[0] ne $bow2{$ID2}[0]) {
			print "\nIDs do not match\n";
			print "$bow1{$ID1}[0]\t$bow1{$ID1}[1]\t$bow2{$ID2}[0]\t$bow2{$ID2}[1]\n"; 
			}
		}
	}
}

exit;

##</code><code>##

IDs do not match
HWUSI-EAS548:7:120:1791:800#0/1         HWUSI-EAS548:7:1:5:1566#0/1     CCACTGTGCTCCAGACTGCGTGACAGAGTGAGACTC

IDs do not match
HWUSI-EAS548:7:120:1791:800#0/1         HWUSI-EAS548:7:1:5:893#0/1      TTTGATGATTTCATTTGATTCCATTCGTTAATGATT

IDs do not match
HWUSI-EAS548:7:120:1791:800#0/1         HWUSI-EAS548:7:1:5:1527#0/1     CGGAGCTTGCAGTGAGCCGAGATCGCGCTACTGCAC

IDs do not match
HWUSI-EAS548:7:120:1791:800#0/1         HWUSI-EAS548:7:1:4:331#0/1      ANTGAGATACCATCTCACGCCAGTCAGACTGGCAAT

IDs do not match
HWUSI-EAS548:7:120:1791:800#0/1         HWUSI-EAS548:7:1:5:1098#0/1     CTTTGCATATTTTGGATAGACACCCAGAAGTGGAAT

IDs do not match
HWUSI-EAS548:7:120:1791:800#0/1         HWUSI-EAS548:7:1:5:877#0/1      AGGCCAGCAGATCACCTGAGGTTGGGAGTTCGAGAC

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1       AATTAGCCAGGTGTGGTGGCGCATGCCTGTAATCCC    HWUSI-EAS548:7:120:1791:900#0/1 ATTCCATTCCATTCCATTCCATTCCATTCCGTTCNG

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1       AATTAGCCAGGTGTGGTGGCGCATGCCTGTAATCCC    HWUSI-EAS548:7:120:1791:800#0/1 TTTAAAAAAAAAAAAAAAAAAAAAAAAATAATTTNT

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1               HWUSI-EAS548:7:1:5:377#0/1      TTCCTTTCAATCATTCCCTTTGATTCCATTCAAAGG

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1               HWUSI-EAS548:7:1:5:1530#0/1     TTCCTGTCGCGTCCATTCCATTCCATTTCACTCCAT

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1               HWUSI-EAS548:7:1:4:12#0/1       CCCTGCGACTTGATNCCCTTAGCTGCTGAAGGACNC

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1               HWUSI-EAS548:7:1:5:1566#0/1     CCACTGTGCTCCAGACTGCGTGACAGAGTGAGACTC

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1               HWUSI-EAS548:7:1:5:893#0/1      TTTGATGATTTCATTTGATTCCATTCGTTAATGATT

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1               HWUSI-EAS548:7:1:5:1527#0/1     CGGAGCTTGCAGTGAGCCGAGATCGCGCTACTGCAC

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1               HWUSI-EAS548:7:1:4:331#0/1      ANTGAGATACCATCTCACGCCAGTCAGACTGGCAAT

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1               HWUSI-EAS548:7:1:5:1098#0/1     CTTTGCATATTTTGGATAGACACCCAGAAGTGGAAT

IDs do not match
HWUSI-EAS548:7:1:5:68#0/1               HWUSI-EAS548:7:1:5:877#0/1      AGGCCAGCAGATCACCTGAGGTTGGGAGTTCGAGAC

IDs do not match
HWUSI-EAS548:7:1:5:377#0/1      TTCCTTTCAATCATTCCCTTTGATTCCATTCAAAGG    HWUSI-EAS548:7:120:1791:900#0/1 ATTCCATTCCATTCCATTCCATTCCATTCCGTTCNG

IDs do not match
HWUSI-EAS548:7:1:5:377#0/1      TTCCTTTCAATCATTCCCTTTGATTCCATTCAAAGG    HWUSI-EAS548:7:120:1791:800#0/1 TTTAAAAAAAAAAAAAAAAAAAAAAAAATAATTTNT

IDs do not match
HWUSI-EAS548:7:1:5:377#0/1      TTCCTTTCAATCATTCCCTTTGATTCCATTCAAAGG    HWUSI-EAS548:7:1:5:68#0/1       AATTAGCCAGGTGTGGTGGCGCATGCCTGTAATCCC

IDs do not match
HWUSI-EAS548:7:1:5:377#0/1              HWUSI-EAS548:7:1:5:1530#0/1     TTCCTGTCGCGTCCATTCCATTCCATTTCACTCCAT

IDs do not match
HWUSI-EAS548:7:1:5:377#0/1              HWUSI-EAS548:7:1:4:12#0/1       CCCTGCGACTTGATNCCCTTAGCTGCTGAAGGACNC

IDs do not match
HWUSI-EAS548:7:1:5:377#0/1              HWUSI-EAS548:7:1:5:1566#0/1     CCACTGTGCTCCAGACTGCGTGACAGAGTGAGACTC

IDs do not match
HWUSI-EAS548:7:1:5:377#0/1              HWUSI-EAS548:7:1:5:893#0/1      TTTGATGATTTCATTTGATTCCATTCGTTAATGATT

##</code><code>##

HWUSI-EAS548:7:1:5:1527#0/1     +       chr12   52084152        CGGAGCTTGCAGTGAGCCGAGATCGCGCTACTGCAC    a`]``_``_```TTXF_[SXU^]aQ`][ZVZVPQ\\    29
HWUSI-EAS548:7:1:5:1098#0/1     +       chr1    245241196       CTTTGCATATTTTGGATAGACACCCAGAAGTGGAAT    ababbabbbbababaaaaYV`baab^aa`WXPN^a`    0
HWUSI-EAS548:7:1:5:877#0/1      +       chr13   40851377        AGGCCAGCAGATCACCTGAGGTTGGGAGTTCGAGAC    a`aaaa^aaaa`b`a`ab^_XZ`a``\`^a`]aRL\    1
HWUSI-EAS548:7:1:4:331#0/1      -       chr13   91090676        ANTGAGATACCATCTCACGCCAGTCAGACTGGCAAT    BB]RXZVVT]aYZYZYY``]Y]^]Y]_]`]`aa__a    0       34:T>N
HWUSI-EAS548:7:1:4:12#0/1       +       chr4    100790527       CCCTGCGACTTGATNCCCTTAGCTGCTGAAGGACNC    aaaaaa`\a```a`B`aa`]_Za]Y_]YQ[OOX`Ba    0       14:G>N,34:T>N
HWUSI-EAS548:7:1:5:1530#0/1     -       chr10   42117291        TTCCTGTCGCGTCCATTCCATTCCATTTCACTCCAT    XXSL]a][`aa^^aaa\_aa`]_`aaa`b^a]_aaa    0       30:T>G,31:A>T
HWUSI-EAS548:7:1:5:893#0/1      +       chr16   44950626        TTTGATGATTTCATTTGATTCCATTCGTTAATGATT    aabaYabaaa`aaa`aa`aaa_aa`aa_`Z]`]a`^    1
HWUSI-EAS548:7:1:5:1566#0/1     -       chr1    36436440        CCACTGTGCTCCAGACTGCGTGACAGAGTGAGACTC    BBBBB\P_WR]YVa^]Z_`bba\^aaaabbab]ab`    0
HWUSI-EAS548:7:1:5:377#0/1      -       chr16   44951483        TTCCTTTCAATCATTCCCTTTGATTCCATTCAAAGG    Y]\W``Ya`Z[`^a[]``[U^a^`_[`aaab``aaa    1
HWUSI-EAS548:7:1:5:68#0/1       +       chr2    68413664        AATTAGCCAGGTGTGGTGGCGCATGCCTGTAATCCC    ``bab`bba`XPa[U[__]a`a_X^a`ZZTZOU^`_    233
HWUSI-EAS548:7:120:1791:926#0/1 -       chr4    48846414        ATTCCATTCCATTCCATTCCATTCCATTCCGTTCNG    `YS^a`]X_``_W`ba^[aaa``bbbaabaaa`aBa    3       1:C>N
HWUSI-EAS548:7:120:1791:800#0/1 -       chr8    13214240        AAAAAAAAAAAAAAAAAAAAAAAAAAAATAATTTNT    aaaaaaaaaaa`aaaaaaaaaa`[`aaaT_[a_aB`    0       1:C>N

##</code><code>##

HWUSI-EAS548:7:1:5:1527#0/1     +       chr12   52084152        CGGAGCTTGCAGTGAGCCGAGATCGCGCTACTGCAC    a`]``_``_```TTXF_[SXU^]aQ`][ZVZVPQ\\    29
HWUSI-EAS548:7:1:5:1098#0/1     +       chr1    245241196       CTTTGCATATTTTGGATAGACACCCAGAAGTGGAAT    ababbabbbbababaaaaYV`baab^aa`WXPN^a`    0
HWUSI-EAS548:7:1:5:877#0/1      +       chr13   40851377        AGGCCAGCAGATCACCTGAGGTTGGGAGTTCGAGAC    a`aaaa^aaaa`b`a`ab^_XZ`a``\`^a`]aRL\    1
HWUSI-EAS548:7:1:4:331#0/1      -       chr13   91090676        ANTGAGATACCATCTCACGCCAGTCAGACTGGCAAT    BB]RXZVVT]aYZYZYY``]Y]^]Y]_]`]`aa__a    0       34:T>N
HWUSI-EAS548:7:1:4:12#0/1       +       chr4    100790527       CCCTGCGACTTGATNCCCTTAGCTGCTGAAGGACNC    aaaaaa`\a```a`B`aa`]_Za]Y_]YQ[OOX`Ba    0       14:G>N,34:T>N
HWUSI-EAS548:7:1:5:1530#0/1     -       chr10   42117291        TTCCTGTCGCGTCCATTCCATTCCATTTCACTCCAT    XXSL]a][`aa^^aaa\_aa`]_`aaa`b^a]_aaa    0       30:T>G,31:A>T
HWUSI-EAS548:7:1:5:893#0/1      +       chr16   44950626        TTTGATGATTTCATTTGATTCCATTCGTTAATGATT    aabaYabaaa`aaa`aa`aaa_aa`aa_`Z]`]a`^    1
HWUSI-EAS548:7:1:5:1566#0/1     -       chr1    36436440        CCACTGTGCTCCAGACTGCGTGACAGAGTGAGACTC    BBBBB\P_WR]YVa^]Z_`bba\^aaaabbab]ab`    0
HWUSI-EAS548:7:1:5:377#0/1      -       chr16   44951483        TTCCTTTCAATCATTCCCTTTGATTCCATTCAAAGG    Y]\W``Ya`Z[`^a[]``[U^a^`_[`aaab``aaa    1
HWUSI-EAS548:7:1:5:68#0/1       +       chr2    68413664        AATTAGCCAGGTGTGGTGGCGCATGCCTGTAATCCC    ``bab`bba`XPa[U[__]a`a_X^a`ZZTZOU^`_    233
HWUSI-EAS548:7:120:1791:900#0/1 -       chr4    48846414        ATTCCATTCCATTCCATTCCATTCCATTCCGTTCNG    `YS^a`]X_``_W`ba^[aaa``bbbaabaaa`aBa    3       1:C>N
HWUSI-EAS548:7:120:1791:800#0/1 -       chr8    13214240        TTTAAAAAAAAAAAAAAAAAAAAAAAAATAATTTNT    aaaaaaaaaaa`aaaaaaaaaa`[`aaaT_[a_aB`    0       1:C>N