With the use of some modules (Text::CSV::Auto to read in the data and Number::Range to process the ranges), the following works ... in a way.

use Modern::Perl;

use Number::Range;
use Text::CSV::Auto qw( process_csv );
use Data::Dump qw /dump/;

my $debug = 0;
my %database;
process_csv('./primary.txt',
    sub {
        my $row = shift;
        push @{$database{$row->{name}}}, [$row->{start}, $row->{end}];
    }
);
say dump(\%database) if $debug;

analyse ('./secondary_1.txt');
analyse ('./secondary_2.txt');

sub analyse {
    my $file = shift;
    my %data;
    process_csv($file,
        sub {
            my $row = shift;
            push @{$data{$row->{name}}}, [$row->{start}, $row->{end}];
        }
    );
    say dump(\%data) if $debug;
    for my $name (sort keys %data) {
        unless ($database{$name}) {
            say "Unknown name '$name'";
            next;
        }
        for my $range_ref (@{$database{$name}}) {
            print "$name: $range_ref->[0] $range_ref->[1] ";
            my $range = Number::Range->new($range_ref->[0] .. $range_r
+ef->[1]);
            for my $testrange_ref (@{$data{$name}}) {
                if ($range->inrange(@$testrange_ref)) {
                    print "present $testrange_ref->[0] $testrange_ref-
+>[1] ";
                }
                else {
                    print "absent 0 0 ";
                }
            }
            print "\n";
        }
    }
}
[download]

Output:

Alex: 3 44 absent 0 0 absent 0 0 
Alex: 124 175 absent 0 0 present 134 155 
Barry: 2 44 present 12 24 
James: 6 45 absent 0 0
Alex: 3 44 absent 0 0 
Alex: 124 175 present 154 174 
Drew: 9 43 present 19 54 absent 0 0 
James: 6 45 present 29 45
[download]

This solution suffers from the same problem you already mentioned: it checks all ranges and finds that some ranges in the secondary files are outside of the ranges in the primary file (see the data for "Alex"). But unless you find a good rule to define which ranges in the secondary files are to be checked against which ranges in the primary files, there is no way to solve this problem.

Oh and BTW, it is "Perl" (the language) or "perl" (the executable), but never ever "PERL". :)

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