Post the code you are using to get that output from that input

use warnings;

open (SourceFile, "$ARGV[0]");
open (TargetFile, ">$ARGV[1]");


while (<SourceFile>) {

# Remove the last character from the line.
#$Line = substr($_,0,-1);
  chomp;
($Year,$HSP_rates,$Curr,$Scenario,$Version,$Product,$CostCenter,$Activ
+ity,$Entity,$Acct,$BegBal,$Jan,$Feb,$Mar,$Apr,$May,$Jun,$Jul,$Aug,$Se
+p,$Oct,$Nov,$Dec) = split(',',$_);
 
  print TargetFile "$Year,";
  print TargetFile "$HSP_rates,";
  print TargetFile "$Curr,";
  print TargetFile "$Scenario,";
  print TargetFile "$Version,";
  print TargetFile "$Product,";
  if( length( $CostCenter ) > 0 )
  {
                                open (MAPFile,"$ARGV[2]");
                while ( <MAPFile> ) {        
                            chomp;
                             my @line = split(',', $_);
                     $hash{$line[0]} = $line[0];
                     $hash1{$line[0]} = $line[2];
                     $hash2{$line[1]} = $line[1];
                                        $hash3{$line[1]} = $line[3];
                                                        
              if( $hash{"$CostCenter"} eq "$CostCenter" and $hash2{"$A
+ctivity"} eq "$Activity")
                          {
                                 $c1 = $hash1{"$CostCenter"} and
                                                        $a1 = $hash3{"
+$Activity"};
                                    goto ed;
                            }
                            else
                            {
                                  $c1 = "$CostCenter";
                                                                 $a1 =
+ "$$Activity";
                                                                      
+       
                              }           
                                                        }    
                

        ed:
     close(MAPFile);
  print TargetFile "$c1,";
  print TargetFile "$a1,";
  print TargetFile "$Entity,";        
  }
if( length( $Acct ) > 0 )
  {                             open (MAPFile,"$ARGV[2]");
                while ( <MAPFile> ) {    
                            
                            chomp;
                             my @line = split(",");
                             $hash{$line[4]} = $line[4];
                             $hash1{$line[4]} = $line[5];
                             $hash2{$line[4]} = $line[5];
                                                        

                            if( $hash{"$Acct"} eq "$Acct" )
                              {
                                         $b1 = $hash1{"$Acct"};
                                    goto ed;
                            }
                            else
                            {
                                 $b1 = "$Acct";
                              }    
                             }
                            
    ed:
     close(MAPFile);
  print TargetFile "$b1,";
  }           
                print TargetFile "$BegBal,";
        print TargetFile "$Jan,";    
        print TargetFile "$Feb,";    
        print TargetFile "$Mar,";
        print TargetFile "$Apr,";
        print TargetFile "$May,";    
        print TargetFile "$Jun,";    
        print TargetFile "$Jul,";    
        print TargetFile "$Aug,";
        print TargetFile "$Sep,";    
        print TargetFile "$Oct,";    
        print TargetFile "$Nov,";    
        print TargetFile "$Dec";
    
    print TargetFile "\n";
}    
close (SourceFile);
close (TargetFile);
[download]

Have you tried the code posted here ?

poj