################################################
# 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 H
+UGO name and gene name.
#Column 3 of file [2] is gene name col 4 [3] is the pathway gene is as
+sociated with

open (DUMMY_GENEFILE, 'DummyGenes.txt') or die "cannot open file conta
+ining 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 H
+UGO 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 o
+f the columns [5]-[8] in the HUGO ID file. 

#check col 6, if found print, if not found, check next column. If neve
+r 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 H
+UGO ID\n";
            
            
    }    
    
    
}
close (DUMMYHUGO);
close (DUMMY_GENEFILE);
close (OUT);
exit;
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