Fair enough. Here's my main code so far: 
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]
I think that I have a problem of line endings or input formatting because I have warnings for unitialized values in: my @str = split(undef,$temp_str)

In reply to Re^4: Human genome array by uvnew
in thread Human genome array by uvnew

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