comment on

I have a file that looks like this:

>34513
-------------------------------MVAIIFDMDGVLYRG
-----N-RAIPGVRELIEF-------LKE-R--------G------
>22476
------------------------------ALKAVLVDLNGTLHI-
--------AVPGAQEALKR---------------------------
>56832
------MARCERLRGA-----ALRDVLG--RAQGVLFDCDGVLWNG-
----E-RAVPGAPELLER-------LAR-------------------
>12543
---------------------------E--QFDILLLDLDGVVYVG-
----D-RLLPGARRALRR----------------------------G
>29078
---------------------------------AVLFDIDGVLVLS-
----W-RAIPGAAETVRQ-------LTH-R--------G--------
[download]

For now, I'm just interested in the 'headers' (that is, the line starting with '>'). I would like to place each of these in a hash and increment a count. So, for example, the header '>34513' would have a count value of '1', the header '>12543' count value 4 and so forth. This is what I've done so far.

#!/usr/local/bin/perl

use strict;
use English;
use Data::Dumper;
use UNIVERSAL qw(isa);
use FileHandle;
use Exception;

my $alignment = shift;

if (!$alignment || ! -e $alignment) {
    die new Exception("couldnt open names file $alignment $!");
}

warn "# Reading alignment data";
my $alignData = getAlignData($alignment);
warn "# Got data: ".scalar (keys %$alignData);

#################################################

sub getAlignData {
    my ($fIn) = @ARG;

    my $fh = new FileHandle($fIn)
        or die "";

    my $count = 0;

        my $hData = {};

    while (my $line = $fh->getline)
    {
        my @cols = split /\s+/, $line;

        # search only for lines with identifier

        my $field = $cols[0];

        my $test = substr($field, 0, 1);

        if("$test" eq ">")
        {
                 $count++;
         my $hEntry = {
            'identifier' => $cols[0],
            'line' => $count,
        };

        my ($record) = sort ($hEntry->{identifier});
        $hData->{$record} = $hEntry;
        }
    }

    foreach my $k ( keys %{$hData} )
    {
        printf "%s -> %s\n", $k, $hData->{$k};
    }

    return $hData;
}
[download]

However, when I try to print out the hash I get the following.

>34513 -> HASH(0x87a3a40)
>22476 -> HASH(0x87a3980)
>56832 -> HASH(0x8762380)
>12543 -> HASH(0x87a3940)
>29078 -> HASH(0x8892b30)
[download]

Can anyone please tell me what I may be doing wrong? Thanks in advance.

In reply to Not able to print out hash contents correctly by Angharad

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