That just means that the order in which you add key/value pairs to a hash is not the order in which they are stored in the hash. Here is an example:

use strict;
use warnings;

$\ = "\n";
$, = ', ';


my %hash = ();
$hash{"h"} = 10;
$hash{"z"} = 20;
$hash{"a"} = 30;

foreach my $key (keys %hash) {
    print "$key: $hash{$key}";
}

--output:--
a: 30
h: 10
z: 20
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However, the key/value pairs are the same. A key will never be associated with a value that you did not enter for that key.

Take a look at this example:

use strict;
use warnings;

$\ = "\n";
$, = ', ';


my %results = ();
my $line = 'HWUSI-EAS548:7:1:5:1527#0/1  + chr12  52084152 CGGAGC';

my @pieces = split /\s+/, $line;
my $id = $pieces[0];
my $seq = $pieces[-1];

$results{$id} = $seq;
foreach my $key (keys %results) {
    print "$key -----> $results{$key}";
}

--output:--
HWUSI-EAS548:7:1:5:1527#0/1 -----> CGGAGC
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If you want to gather all the sequences corresponding to an id, you can do this:

use strict;
use warnings;

$\ = "\n";
$, = ', ';


my %results = ();
while (<DATA>) {
    my @pieces = split /\s+/;
    my $id = $pieces[0];
    my $seq = $pieces[-1];
    $results{$id} = [] unless exists $results{$id};
    push @{$results{$id}}, $seq;
}

foreach my $key (keys %results) {
    my $arr_str = join ',', @{$results{$key}};
    print "$key -----> [$arr_str]";
}

__DATA__
HWUSI-EAS548:7:1:5:1527#0/1  + chr12  52084152 CGGAGC
HWUSI-EAS548:7:1:5:1527#0/1  + chr12  52084152 XXXXXX
Some_other_id  + chr12  52084152 CGGAGC
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You might want to experiment a little more with hashes in a separate practice program. For instance, you might want to read perlintro and perldsc, which you can read by typing:

$ man perlintro

or

$ man perdsc
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For a complete list of topics available type:

$man perl
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and scroll down.

while (<DATA>) {
    my @pieces = split /\s+/;
    my $id = $pieces[0];
    my $seq = $pieces[-1];
    $results{$id} = [] unless exists $results{$id};
    push @{$results{$id}}, $seq;
}
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Actually, as perlreftut instructs, the line:

 $results{$id} = [] unless exists $results{$id};
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is unnecessary. I highly recommend that you read perlreftut:

$ man perlreftut

I take it this is bowtie output? It makes no sense to me why you are comparing all IDs in the first file to all IDs in the second? The whole point of using a hash is that you can look up specific keys, whereas an array would be for storing an ordered list.

What are you actually trying to do? Get the common IDs between the files and say whether their associated sequences match? You can try something like this for that :

foreach my $id (keys %hash1){ # you can use (sort keys %hash1) if you 
+want them in a specified order
   if ( exists $hash2{$id} ){
      print "\'$id\' exists in both hashes.\n";
      if ( $hash1{$id} eq $hash2{$id} ){
         ## id and sequence are stored as key value pairs
         print "and the sequences match too.\n";
      }
      else{
         print "but the sequences do not match.\n";
      }
   }
   else {
      print "\'$id\' only exists in hash1.\n";
}

}
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If you want help with data strucutes, try perldsc for starters.

Hello BioLion,

Basically I followed your code,

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 sequen
+ces match $bow1{$Seq1} $bow2{$Seq2} \n";
      }
      else{
        print "$bow1{$ID1} exists in $file1 and $file2 but sequences D
+O NOT match $bow1{$Seq1} $bow2{$Seq2} \n";
      }
   }
   else {
      print "$bow1{$ID1} only exists in $file1 .\n";
}

}



exit;
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However I get some errors

Global symbol "$ID2" requires explicit package name at /home/choia2/sc
+ripts/BowtieCompare.pl line 50.
Global symbol "$ID2" requires explicit package name at /home/choia2/sc
+ripts/BowtieCompare.pl line 51.
Global symbol "$Seq1" requires explicit package name at /home/choia2/s
+cripts/BowtieCompare.pl line 53.
Global symbol "$Seq2" requires explicit package name at /home/choia2/s
+cripts/BowtieCompare.pl line 53.
Global symbol "$Seq1" requires explicit package name at /home/choia2/s
+cripts/BowtieCompare.pl line 56.
Global symbol "$Seq2" requires explicit package name at /home/choia2/s
+cripts/BowtieCompare.pl line 56.
Execution of /home/choia2/scripts/BowtieCompare.pl aborted due to comp
+ilation errors.
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Basically the foreach loop.. I never used hash for other programming languages (I wasn't professional though) but this hash concept is confusing.. could you help me one more time? >.<

Could you please take a look at this and let me know if there's any logical error? I think it works well.. Also if you can give me any suggestions, please do not hesitate to reply / message. Thank you so much!! (***Special thanks to BioLion! You're awesome :D***)

#!/usr/bin/perl
use warnings; # Perl interpreter command
use strict;


my %bow1 = ();
my $file1 = shift;
open (FILE1, "$file1")|| die "Failed to open $file1 for reading : $!";
+ # Open first file

while (<FILE1>) { # Reading first hash
    my ($ID, undef, undef, undef, $Seq) = split;
    $bow1{$ID}[0] = $ID;
    $bow1{$ID}[1] = $Seq;
}
close FILE1 || die "Failed to close $file1 : $!";


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

open (FILE2, "$file2") || die "Failed to open $file2 for reading : $!"
+; # Open first file

while (<FILE2>) { # Reading second hash
    my ($ID, undef, undef, undef, $Seq) = split;
    $bow2{$ID}[0] = $ID;
    $bow2{$ID}[1] = $Seq;
}
close FILE2 || die "Failed to close $file2 : $!";


print"Match status\t$file1 ID\t$file1 Sequence\t$file2 ID\t$file2 Sequ
+ence\n"; # Print title

my $totalCount=0; #initialize variables for counting
my $identical=0;
my $diffSeq=0;
my $unique=0;

foreach my $ID (keys %bow1){ # can use (sort keys %hash) to put items 
+in a specified order
   if (exists $bow2{$ID}[0] ){
      if ( $bow1{$ID}[0] eq $bow2{$ID}[0] ){
         ## id and sequence are stored as key value pairs
          if ( $bow1{$ID}[1] eq $bow2{$ID}[1] ){
         #print "Identical\t$bow1{$ID}[0]\t$bow1{$ID}[1]\t$bow2{$ID}[0
+]\t$bow2{$ID}[1]\n"; #display ID and sequences  -->too many: commente
+d out
         $identical=$identical+1; #count identical pairs
         }
         else{
        print "SameID, DiffSeq\t$bow1{$ID}[0]\t$bow1{$ID}[1]\t$bow2{$I
+D}[0]\t$bow2{$ID}[1]\n"; #display ID and sequences
        $diffSeq=$diffSeq+1; #count pairs with different sequences but
+ identical IDs
        }
      }
    }
    else {
    print "Unique\t$bow1{$ID}[0]\t$bow1{$ID}[1]\t - \t - \n"; #display
+ ID and sequences
    $unique=$unique+1; #count unique IDs from first file
    }
}
$totalCount = $identical + $diffSeq + $unique; #total count - should m
+atch with total ID in first file
print "Identical\tSeq is different\tUnique in $file1\tTotal\n"; #print
+ title
print "$identical\t$diffSeq\t$unique\t$totalCount\n"; #print numbers

exit;
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