while (<FILE1>)
{
    if ($_ =~ />/) #Header
    {
        if ($chr_num > 0)
        {
            my @str = split(undef,$temp_str);
            push (@genome,@str);
        }
        $chr_num++;
        print $chr_num . "\n";
        $temp_str = "";
    }
    else
    {
        my $temp = chomp($_);
        $temp_str = $temp_str . $temp;        
    }
}
[download]

To get rid of the Use of uninitialized value in regexp compilation warning message, I think you want to use:

my @str = split //, $temp_str;
[download]

This will split a string into individual characters.

That's better, but it would be even better if posted code that was self contained. Also, as many will mention, always use strict; and use warnings; unless you have a specific reason you're not. I know you're using them, but you should show us you're using them.

The main problem I'm seeing in your script is that you're pushing a list into an array. Your description implies you want a matrix. In order to do that, you'll have to push an array reference into your @genome array:

push (@genome,\@str);

Perl only stores scalars in arrays and hash values, so, in order to create a multi-level datastructure, you need fill the array with a reference to the array.

A minor thing is that you'll probably miss your last chromosome because of how you're parsing the file. After you hit the end of the file, and there isn't a dangling header, you'll still have a lot of data in $temp_str that doesn't make it into @genome.

Edit: also, as toolic says, you should change you split line to:

my @str = split //, $temp_str;

Hi, uvnew!

Perhaps you could elucidate why the answers to your previous post (from 8 months ago) Bioinformatic task failed to solve your problem?

Meanwhile, I suggest that you consult the documentation for split.

hth, dave