Dear perl monks, I started self-learning perl because of my job (I'm a biochemist student who needs to handle huge txt files, 3Gb each) I need to compare two files and they're in the same format. I'm still confused with these hashes and I wrote an inefficient code. What I want is first column (ID) and 5th column (sequence) from each file and compare them. 1)Check ID names 2)If they dont match, print both ID and the sequences from each file 3)If they match, and the sequences match, do not print 4)If they match, but the sequences do not match, print both ID and the sequences from each file This is what I'm trying to do. I do not have any syntax errors, but I get a weird output. I'd very appriciate if you could help me out ASAP! Thank you very much =) 
#!/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$bo
+w2{$ID2}[1]\n"; 
            }
        }
    }
}

exit;

[download]
UPDATE :My current output is like: 
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 ATTCCATTCCATTCCATTCCATTCCATTCCGTTCN
+G

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

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 ATTCCATTCCATTCCATTCCATTCCATTCCGTTCN
+G

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

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

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

[download]
Input file one: 
HWUSI-EAS548:7:1:5:1527#0/1     +       chr12   52084152        CGGAGC
+TTGCAGTGAGCCGAGATCGCGCTACTGCAC    a`]``_``_```TTXF_[SXU^]aQ`][ZVZVPQ\
+\    29
HWUSI-EAS548:7:1:5:1098#0/1     +       chr1    245241196       CTTTGC
+ATATTTTGGATAGACACCCAGAAGTGGAAT    ababbabbbbababaaaaYV`baab^aa`WXPN^a
+`    0
HWUSI-EAS548:7:1:5:877#0/1      +       chr13   40851377        AGGCCA
+GCAGATCACCTGAGGTTGGGAGTTCGAGAC    a`aaaa^aaaa`b`a`ab^_XZ`a``\`^a`]aRL
+\    1
HWUSI-EAS548:7:1:4:331#0/1      -       chr13   91090676        ANTGAG
+ATACCATCTCACGCCAGTCAGACTGGCAAT    BB]RXZVVT]aYZYZYY``]Y]^]Y]_]`]`aa__
+a    0       34:T>N
HWUSI-EAS548:7:1:4:12#0/1       +       chr4    100790527       CCCTGC
+GACTTGATNCCCTTAGCTGCTGAAGGACNC    aaaaaa`\a```a`B`aa`]_Za]Y_]YQ[OOX`B
+a    0       14:G>N,34:T>N
HWUSI-EAS548:7:1:5:1530#0/1     -       chr10   42117291        TTCCTG
+TCGCGTCCATTCCATTCCATTTCACTCCAT    XXSL]a][`aa^^aaa\_aa`]_`aaa`b^a]_aa
+a    0       30:T>G,31:A>T
HWUSI-EAS548:7:1:5:893#0/1      +       chr16   44950626        TTTGAT
+GATTTCATTTGATTCCATTCGTTAATGATT    aabaYabaaa`aaa`aa`aaa_aa`aa_`Z]`]a`
+^    1
HWUSI-EAS548:7:1:5:1566#0/1     -       chr1    36436440        CCACTG
+TGCTCCAGACTGCGTGACAGAGTGAGACTC    BBBBB\P_WR]YVa^]Z_`bba\^aaaabbab]ab
+`    0
HWUSI-EAS548:7:1:5:377#0/1      -       chr16   44951483        TTCCTT
+TCAATCATTCCCTTTGATTCCATTCAAAGG    Y]\W``Ya`Z[`^a[]``[U^a^`_[`aaab``aa
+a    1
HWUSI-EAS548:7:1:5:68#0/1       +       chr2    68413664        AATTAG
+CCAGGTGTGGTGGCGCATGCCTGTAATCCC    ``bab`bba`XPa[U[__]a`a_X^a`ZZTZOU^`
+_    233
HWUSI-EAS548:7:120:1791:926#0/1 -       chr4    48846414        ATTCCA
+TTCCATTCCATTCCATTCCATTCCGTTCNG    `YS^a`]X_``_W`ba^[aaa``bbbaabaaa`aB
+a    3       1:C>N
HWUSI-EAS548:7:120:1791:800#0/1 -       chr8    13214240        AAAAAA
+AAAAAAAAAAAAAAAAAAAAAATAATTTNT    aaaaaaaaaaa`aaaaaaaaaa`[`aaaT_[a_aB
+`    0       1:C>N

[download]
Input file two:
HWUSI-EAS548:7:1:5:1527#0/1     +       chr12   52084152        CGGAGC
+TTGCAGTGAGCCGAGATCGCGCTACTGCAC    a`]``_``_```TTXF_[SXU^]aQ`][ZVZVPQ\
+\    29
HWUSI-EAS548:7:1:5:1098#0/1     +       chr1    245241196       CTTTGC
+ATATTTTGGATAGACACCCAGAAGTGGAAT    ababbabbbbababaaaaYV`baab^aa`WXPN^a
+`    0
HWUSI-EAS548:7:1:5:877#0/1      +       chr13   40851377        AGGCCA
+GCAGATCACCTGAGGTTGGGAGTTCGAGAC    a`aaaa^aaaa`b`a`ab^_XZ`a``\`^a`]aRL
+\    1
HWUSI-EAS548:7:1:4:331#0/1      -       chr13   91090676        ANTGAG
+ATACCATCTCACGCCAGTCAGACTGGCAAT    BB]RXZVVT]aYZYZYY``]Y]^]Y]_]`]`aa__
+a    0       34:T>N
HWUSI-EAS548:7:1:4:12#0/1       +       chr4    100790527       CCCTGC
+GACTTGATNCCCTTAGCTGCTGAAGGACNC    aaaaaa`\a```a`B`aa`]_Za]Y_]YQ[OOX`B
+a    0       14:G>N,34:T>N
HWUSI-EAS548:7:1:5:1530#0/1     -       chr10   42117291        TTCCTG
+TCGCGTCCATTCCATTCCATTTCACTCCAT    XXSL]a][`aa^^aaa\_aa`]_`aaa`b^a]_aa
+a    0       30:T>G,31:A>T
HWUSI-EAS548:7:1:5:893#0/1      +       chr16   44950626        TTTGAT
+GATTTCATTTGATTCCATTCGTTAATGATT    aabaYabaaa`aaa`aa`aaa_aa`aa_`Z]`]a`
+^    1
HWUSI-EAS548:7:1:5:1566#0/1     -       chr1    36436440        CCACTG
+TGCTCCAGACTGCGTGACAGAGTGAGACTC    BBBBB\P_WR]YVa^]Z_`bba\^aaaabbab]ab
+`    0
HWUSI-EAS548:7:1:5:377#0/1      -       chr16   44951483        TTCCTT
+TCAATCATTCCCTTTGATTCCATTCAAAGG    Y]\W``Ya`Z[`^a[]``[U^a^`_[`aaab``aa
+a    1
HWUSI-EAS548:7:1:5:68#0/1       +       chr2    68413664        AATTAG
+CCAGGTGTGGTGGCGCATGCCTGTAATCCC    ``bab`bba`XPa[U[__]a`a_X^a`ZZTZOU^`
+_    233
HWUSI-EAS548:7:120:1791:900#0/1 -       chr4    48846414        ATTCCA
+TTCCATTCCATTCCATTCCATTCCGTTCNG    `YS^a`]X_``_W`ba^[aaa``bbbaabaaa`aB
+a    3       1:C>N
HWUSI-EAS548:7:120:1791:800#0/1 -       chr8    13214240        TTTAAA
+AAAAAAAAAAAAAAAAAAAAAATAATTTNT    aaaaaaaaaaa`aaaaaaaaaa`[`aaaT_[a_aB
+`    0       1:C>N

[download]

In reply to how to compare two hashes with perl? by FluffyBunny

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