################################################
# Declare an outfile to print to
my $outfile = "HUGO_dummyResults.txt";

# Open the outfile using a file handle
open( OUT, "> $outfile" ) or die "cannot create the output file";

#################################################

# Open file of list of neurotransmission genes where ENST has not been found

# FILENOTES::: File created in access using a query against approved HUGO name and gene name.
#Column 3 of file [2] is gene name col 4 [3] is the pathway gene is associated with

open (DUMMY_GENEFILE, 'DummyGenes.txt') or die "cannot open file containing genes";

#################################################

# 2- Open HUGO tabbed file
# FILENOTES::::	Approved gene name is in col 2 [1]

open (DUMMYHUGO,'DummyHugo.txt') or die "cannot open file containing HUGO IDs";

#################################################
#Operations
#################################################

#make array genes
#@genes = DUMMY_GENEFILE;		#No longer done here, see below

#make array HUGO
@hugo = DUMMYHUGO;

#for each line in genefile, try to match gene name [2] to one column of the columns [5]-[8] in the HUGO ID file. 

#check col 6, if found print, if not found, check next column. If never found, print "not found".

foreach (<DUMMY_GENEFILE>) #Changed from (<DUMMY_GENEFILE>)

{
	#make array genes
	@genes = DUMMY_GENEFILE;
	
	for ($i = 4; $i < @hugo; $i++)
	
	{
		if ($genes[2] eq $hugo[$i])

			#If found first print result
				
				{
						
					print OUT "$genes[0]\t$genes[1]\t$genes[2]\tgenes[3]\t$hugo[1]\n";
					
								
				}
			
			# HUGO ID not found, print
			print OUT "$genes[0]\t$genes[1]\t$genes[2]\tgenes[3]\tNo HUGO ID\n";
			
			
	}	
	
	
}
close (DUMMYHUGO);
close (DUMMY_GENEFILE);
close (OUT);
exit;