Hi ccelt09,

In truth I couldn't quite work out what your code was trying to do. But your description of what you wanted to accomplish seemed clear. Below is a different take on how to sort your input into separate files. It could be easily done with fewer CPAN modules, but I reached for them anyway. So to use this code you'd have to install the following from CPAN:

 Text::CSV_XS DBI DBD::CSV

If that's not a problem, then the following code should work well for you:

use strict;
use warnings;
use Text::CSV;
use DBI;

# input filename, and output file template with %d for interval #
my $input_filename = 'td.data';
my $output_filename = 'split_%d.data';

# Divide loci into groups of one million per output file
sub calculate_interval { return int((shift) / 1000000) };

my $dbh = DBI->connect ("dbi:CSV:", undef, undef, {
    csv_eol          => "\n",
    csv_sep_char     => "\t",
    csv_class        => "Text::CSV_XS",
    csv_null         => 1,
    csv_tables       => { genetics => {
                f_file => $input_filename,,
                col_names => [qw(a b c d locus f g h i j k l m n o)],
                }},
    RaiseError       => 1,
    PrintError       => 1,
}) or die $DBI::errstr;

# Magic
my $sth = $dbh->prepare("select * from genetics order by locus");
$sth->execute;

# Grunt work to output into separate files
$, = "\t";
my $output;
my $output_interval = -1;
while (my @row = $sth->fetchrow_array) {
    my $interval = calculate_interval $row[4];
    if ($interval ne $output_interval) {
        $output_interval = $interval;
        open $output, '>', sprintf($output_filename, $interval)
            or die "$output_filename $!";
    }    
        print $output @row, "\n";
}
[download]

With this input data in a file named td.data:

0    50    4    46    723430    0    2    1    2    1    1    1    1  
+  3    1
0    50    4    46    5533723430    0    2    1    2    1    1    1   
+ 1    3    1
0    50    4    46    33723430    0    2    1    2    1    1    1    1
+    3    1
0    50    2    48    654732    0    1    1    1    0    2    3    2  
+  1    3
[download]

This was the result:

split_0.data:0    50    2    48    654732    0    1    1    1    0    
+2    3    2    1    3    
split_0.data:0    50    4    46    723430    0    2    1    2    1    
+1    1    1    3    1    
split_33.data:0    50    4    46    33723430    0    2    1    2    1 
+   1    1    1    3    1    
split_5533.data:0    50    4    46    5533723430    0    2    1    2  
+  1    1    1    1    3    1
[download]