!#/usr/bin/perl -w

open (IN, "C:/Work/Cytokine/ING_cytokines_20080805.txt");

while (<IN>){ #start while loop
	  chomp;
	  @t=split(/\t/,$_);   	   #splits file and stores values in $_
	  $ING{$t[9]}=1;		   #selects one column from input file
 } # end while loop
close IN;	  

open (OUT, ">C:/work/Cytokine/Cytokine.txt") or die "cannot open";
open (IN, "C:/work/Cytokine/CytokineArrays.txt") or die "cannot open";

while(<IN>){ #start of while loop	   
	 chomp;
	 @cytokine=split(/\t/,$_);		   #splits input file and stores in $_
	 #begin if statements
	 
	 if($cytokine[1]=~/\S+/ and exists $ING{$cytokine[1]}){	  #group 1 - compares second row of input file to $ING
	 	print OUT "$cytokine[0]\t$cytokine[1]\tY\t";
		$SABioY++;}
	 elsif ($cytokine[1] =~ /\d+/) {
	 	   print OUT "$cytokine[0]\t$cytokine[1]\tN\t";
		   $SABioN++;}
		else {
		    print OUT "$cytokine[0]\t$cytokine[1]\t\t";
		}	     
   	  if ($SABioY ge 0) {print OUT "SA Biosciences has $SABioY products."};
      if ($SABioN ge 0) {print OUT "SA Biosciences does not have $SABioN products."};
		
	 if($cytokine[3]=~/\S+/ and exists $ING{$cytokine[3]}){	  #group 2 
	 	print OUT "$cytokine[2]\t$cytokine[3]\tY\t";}
	 elsif ($cytokine[3] =~ /\d+/) {
	 	   print OUT "$cytokine[2]\t$cytokine[3]\tN\t";
		}else {
		    print OUT "$cytokine[2]\t$cytokine[3]\t\t";
		}	  
	
	 if($cytokine[5]=~/\S+/ and exists $ING{$cytokine[5]}){	  #group 3 
	 	print OUT "$cytokine[4]\t$cytokine[5]\tY\t";}
	 elsif ($cytokine[5] =~ /\d+/) {
	 	   print OUT "$cytokine[4]\t$cytokine[5]\tN\t";
		}else {
		    print OUT "$cytokine[4]\t$cytokine[5]\t\t";
		}	
	 	   	
	 if($cytokine[7]=~/\S+/ and exists $ING{$cytokine[7]}){	  #group 4 
	 	print OUT "$cytokine[6]\t$cytokine[7]\tY\t";}
	 elsif ($cytokine[7] =~ /\d+/) {
	 	   print OUT "$cytokine[6]\t$cytokine[7]\tN\t";
		}else {
		    print OUT "$cytokine[6]\t$cytokine[7]\t\t";
		}  
	
	 if($cytokine[9]=~/\S+/ and exists $ING{$cytokine[9]}){	  #group 5
	 	print OUT "$cytokine[8]\t$cytokine[9]\tY\t";}
	 elsif ($cytokine[9] =~ /\d+/) {
	 	   print OUT "$cytokine[8]\t$cytokine[9]\tN\t";
		}else {
		    print OUT "$cytokine[8]\t$cytokine[9]\t\t";
		}  
	 
	 if($cytokine[11]=~/\S+/ and exists $ING{$cytokine[11]}){	  #group 6
	 	print OUT "$cytokine[10]\t$cytokine[11]\tY\t";}
	 elsif ($cytokine[11] =~ /\d+/) {
	 	   print OUT "$cytokine[10]\t$cytokine[11]\tN\t";
		}else {
		    print OUT "$cytokine[10]\t$cytokine[11]\t\t";
		}  
	 
	 if($cytokine[13]=~/\S+/ and exists $ING{$cytokine[13]}){	  #group 7
	 	print OUT "$cytokine[12]\t$cytokine[13]\tY\t";}
	 elsif ($cytokine[13] =~ /\d+/) {
	 	   print OUT "$cytokine[12]\t$cytokine[13]\tN\t";
		}else {
		    print OUT "$cytokine[12]\t$cytokine[13]\t\t";
		} 
	    
	 if($cytokine[15]=~/\S+/ and exists $ING{$cytokine[15]}){	  #group 8
	 	print OUT "$cytokine[14]\t$cytokine[15]\tY\t";}
	 elsif ($cytokine[15] =~ /\d+/) {
	 	   print OUT "$cytokine[14]\t$cytokine[15]\tN\t";
		}else {
		    print OUT "$cytokine[14]\t$cytokine[15]\t\t";
		} 
		 
	 if($cytokine[17]=~/\S+/ and exists $ING{$cytokine[17]}){	  #group 9
	 	print OUT "$cytokine[16]\t$cytokine[17]\tY\t";}
	 elsif ($cytokine[17] =~ /\d+/) {
	 	   print OUT "$cytokine[16]\t$cytokine[17]\tN\t";
		}else {
		    print OUT "$cytokine[16]\t$cytokine[17]\t\t";
		} 
	 	 
 	 if($cytokine[19]=~/\S+/ and exists $ING{$cytokine[19]}){	  #group 10
	 	print OUT "$cytokine[16]\t$cytokine[19]\tY\t";}
	 elsif ($cytokine[19] =~ /\d+/) {
	 	   print OUT "$cytokine[18]\t$cytokine[19]\tN\t";
		}else {
		    print OUT "$cytokine[18]\t$cytokine[19]\t\t";
		} 
	 
	 if($cytokine[21]=~/\S+/ and exists $ING{$cytokine[21]}){	  #group 11
	 	print OUT "$cytokine[20]\t$cytokine[21]\tY\t";}
	 elsif ($cytokine[21] =~ /\d+/) {
	 	   print OUT "$cytokine[20]\t$cytokine[21]\tN\t";
		}else {
		    print OUT "$cytokine[20]\t$cytokine[21]\t\t";
		} 
	 
	 if($cytokine[23]=~/\S+/ and exists $ING{$cytokine[23]}){	  #group 12 (\n used in the final group for formatting)
	 	print OUT "$cytokine[22]\t$cytokine[23]\tY\t\n";}
	 elsif ($cytokine[23] =~ /\d+/) {
	 	   print OUT "$cytokine[22]\t$cytokine[23]\tN\t\n";
		}else {
		    print OUT "$cytokine[22]\t$cytokine[23]\t\t\n";
		}
		
}  # end of while loop


close IN;
close OUT;