#!/usr/bin/perl
use strict;
use warnings;
use Data::Dumper;


=cut
open( my $in, "c:/Documents and Settings/mydir/Desktop/current/mart_export.txt" );
open( my $out, ">c:/Documents and Settings/mydir/Desktop/current/clone_qual_counts.txt" );

my $first_line = <$in>;
chomp $first_line;

my %clone_hash;
print $out "clone\tgood\tbad\n";
while (<$in>)
{
    chomp;
	my @fields = split /\t/; 		
	my ($gene_symbol, $esc_qc) = ($fields[1], $fields[8]);
	#use regex to extend to a hash of hashes to separate good and bad clone counts
	my $grade = ($esc_qc =~ /^pass[1-3]$/) ? 'good' : 'bad';
	$clone_hash{$gene_symbol}{$grade}++;
}
for (keys %clone_hash) {
	#print $out "$_ \t $clone_hash{$_}{good}\n" if exists $clone_hash{$_}{good};
	print $out "$_ \t$clone_hash{$_}{good}\n" if exists $clone_hash{$_}{good};
	#print $out "\t$clone_hash{$_}->{'bad'}\n";
}
#print Dumper(\%clone_hash);

close ($in);
close ($out);