#!/usr/bin/env perl -l

use strict;
use warnings;

my %count;

while (<DATA>) {
    my ($seq, $chr, $loc) = split;
    #push @{$count{$chr}{$loc}}, $seq;
    ++$count{$chr}{$loc};
}

print 'Reads by specific chromosome and location:';
my @wanted = ([qw{chr1 100}], [qw{chr1 500}], [qw{chr2 200}], [qw{chr3 100}]);

for (@wanted) {
    print "Reads on CHR:$_->[0] LOC:$_->[1] = ", get_loc_reads(@$_);
}

print 'Reads with positive counts by chromosome and location:';
get_read_counts();

sub get_loc_reads {
    my ($chr, $loc) = @_;
    #return exists $count{$chr}{$loc} ? scalar @{$count{$chr}{$loc}} : 0;
    return exists $count{$chr}{$loc} ? $count{$chr}{$loc} : 0;
}

sub get_read_counts {
    for my $chr (sort keys %count) {
        for my $loc (sort keys %{$count{$chr}}) {
            #print "Reads on CHR:$chr LOC:$loc = ", scalar @{$count{$chr}{$loc}};
            print "Reads on CHR:$chr LOC:$loc = ", $count{$chr}{$loc};
        } 
    }
}

__DATA__
A chr1 100
B chr1 100
C chr1 100
D chr1 200
E chr1 300
F chr1 300
G chr1 300
H chr2 100
I chr2 200
J chr2 200

##</code><code>##

Reads by specific chromosome and location:
Reads on CHR:chr1 LOC:100 = 3
Reads on CHR:chr1 LOC:500 = 0
Reads on CHR:chr2 LOC:200 = 2
Reads on CHR:chr3 LOC:100 = 0
Reads with positive counts by chromosome and location:
Reads on CHR:chr1 LOC:100 = 3
Reads on CHR:chr1 LOC:200 = 1
Reads on CHR:chr1 LOC:300 = 3
Reads on CHR:chr2 LOC:100 = 1
Reads on CHR:chr2 LOC:200 = 2

##</code><code>##

    push @{$count{$chr}{$loc}}, $seq;
    #++$count{$chr}{$loc};
...
    return exists $count{$chr}{$loc} ? scalar @{$count{$chr}{$loc}} : 0;
    #return exists $count{$chr}{$loc} ? $count{$chr}{$loc} : 0;
...
            print "Reads on CHR:$chr LOC:$loc = ", scalar @{$count{$chr}{$loc}};
            #print "Reads on CHR:$chr LOC:$loc = ", $count{$chr}{$loc};