#!/usr/bin/perl -w
use strict;
#open file
open(my $in,"/Users/mgavibrathwaite/Desktop/CCDS.current.txt") or die " Can't open file: $!";
#open out file
open(OUT, ">/Users/mgavibrathwaite/Desktop/genesperchrcnt.txt");
# initialize the hash
my %geneids=();
#open the file and push the info from the designated columns into it
# remove header
my $firstline = <$in>;
chomp $firstline;
while(<$in>){
	chomp; # remove the newline character
	my @fields = split (/\t/);
	#extract the columns that we are interested in.
	# Populate the key value pairs of the hash with $gene and $id
	$geneids{$fields[2]} = $fields[0];
	# initialize an array to store hash values
	my @chr;
	push @chr, $fields[0];
	#count chromosome number which is the value in the hash
	$geneids{$fields[0]}++;
	next if $geneids{$fields[0]} > 1;
}
foreach my $geneid (
    sort { $geneids{$a} <=> $geneids{$b} } keys %geneids
) {
    print OUT "Chromosome $geneid has $geneids{$geneid} genes\n"; 
}
close($in);
close(OUT);
=cut
Output
Chromosome  has X genes
Chromosome KLHL13 has X genes
Chromosome UTY has Y genes
Chromosome SPIN2B has X genes
Chromosome PIR has X genes
Chromosome ADRBK2 has 22 genes
Chromosome SLC2A11 has 22 genes
Chromosome SELO has 22 genes
Chromosome PIK3IP1 has 22 genes
Chromosome 21 has 323 genes
Chromosome 18 has 358 genes
Chromosome 13 has 402 genes
Chromosome 22 has 553 genes
Chromosome 20 has 724 genes
Chromosome 15 has 733 genes
Chromosome 14 has 772 genes
Chromosome 8 has 827 genes
Chromosome 4 has 922 genes
Chromosome 9 has 982 genes
Chromosome 10 has 1007 genes
Chromosome 16 has 1009 genes
Chromosome X has 1045 genes
Chromosome 5 has 1054 genes
Chromosome 7 has 1137 genes
Chromosome 12 has 1283 genes
Chromosome 6 has 1298 genes
Chromosome 3 has 1354 genes
Chromosome 17 has 1412 genes
Chromosome 11 has 1543 genes
Chromosome 2 has 1624 genes
Chromosome 19 has 1660 genes
Chromosome 1 has 2611 genes