i have tried ur links and put some debug but it seem the second if doesnt encounter. only n times display of "into the second loop .." please fine the full code

#! C:/perl/bin/perl.exe

use strict;
use warnings;
use File::Copy;
use File::Basename;
use Cwd;
use Data::Dumper;
use File::Copy::Recursive qw(dircopy) ;

my $fullpath = cwd();
my $value = 0;
my $file = basename($fullpath);
my $dir = dirname($fullpath);
print("$fullpath, $file, $dir");

opendir(my $pathindex, $dir ) or die "Couldn't read index : $!\n";
while (my $currentfile = readdir($pathindex)) {
         print "\nCurrent Directory File $value\t";
         print "$currentfile","\n";
     $value++;
}

print "\nENTER THE PROJECT NAME FROM ABOVE LIST\n";
my $projectdir = <STDIN>;
chop($projectdir);
my $projectdirpath = "/"."$projectdir";
my $workingdirectory = ($dir.$projectdirpath);
chdir($workingdirectory."/trunk"); 
my $newpath = cwd();

my $source_dirrtl;
my $target_dirrtl ;            # = ("$newpath"."/rtl2");
opendir(my $index, $newpath ) or die "Couldn't read index : $!\n";
while (my $file = readdir($index)) {
       if ($file eq "rtl" ) {
         if(chdir($newpath."/rtl")) {
          my $currentworkingdir = cwd();
          $source_dirrtl = $currentworkingdir;
          $target_dirrtl = ("$newpath"."/rtl2"); 
      }
         last;
     }     

     elsif ($file eq "vhdl") {
         if(chdir($newpath."/vhdl")) {
          my $currentworkingdir = cwd();
          $source_dirrtl =   $currentworkingdir;
          $target_dirrtl = ("$newpath"."/vhdl2"); 
      }
         last;
     }
}
closedir($index);
my $configdirc = $newpath."/configdir";
chdir($configdirc);
opendir( my $indexconfig,$configdirc ) or die "Couldn't enter config d
+irectory: $!\n";
          print("\nCONFIGURATION FILES IN THE CONFIG DIRECTORY \n");
          my @rtlfilelist = glob "*.icfg";
          print ("\n@rtlfilelist \n");

closedir($indexconfig);

my $cChipId;
my $cSubVersId;
my %data_ids;
my $readline;
my $toplevelentity;
my $ivariant_name;
print "\nENTER THE CONFIGURATION FILE NAME FROM THE ABOVE LIST \n";
my $configfile = <STDIN>;
open (my $CFILE,$configfile ) || die "couldnt open file: $!";  
   while ($readline = <$CFILE>) {
       chomp $readline;
       my ($key , $value) = (split /::/, $readline);
       $data_ids{$key} = $value if $key;
       next if $readline =~ /^ $/;
   }
   close($CFILE); 
   for my $key (keys %data_ids) {
       $cChipId = $data_ids{'chipid'};
       $cSubVersId = $data_ids{'subversid'};
       $toplevelentity = $data_ids{'Top_level_entity'};
       $ivariant_name = $data_ids{'Variant_Name'};
   }


my $source_dirsim = ("$newpath"."/sim");
my $target_dirsim1 = ("$newpath"."/sim2");


my $source_dirsynth;
my $target_dirsynth1 ;
opendir(my $indexs, $newpath ) or die "Couldn't read indexs : $!\n";
while (my $file = readdir($indexs)) {
       if ($file eq "par" ) {
         if(chdir($newpath."/par")) {
          my $currentworkingdir = cwd();
          $source_dirsynth = $currentworkingdir;
          $target_dirsynth1 = ("$newpath"."/par2"); 
      }
         last;
     }     

     elsif ($file eq "synth") {
         if(chdir($newpath."/synth")) {
          my $currentworkingdir = cwd();
          $source_dirsynth =   $currentworkingdir;
          $target_dirsynth1 = ("$newpath"."/synth2"); 
      }
         last;
     }
}
closedir($indexs);




mkdir($target_dirrtl,0777);
mkdir($target_dirsim1,0777);
mkdir($target_dirsynth1,0777);




my $filertl = dircopy($source_dirrtl, $target_dirrtl);
my $filesim = dircopy($source_dirsim, $target_dirsim1);
my $filesynth = dircopy($source_dirsynth, $target_dirsynth1);



opendir $source_dirsynth: $!";

chdir("$target_dirrtl");
my $m4file = "$projectdir".".m4";
open(MYFILE,">>$m4file"); 
  print MYFILE ("define(`m4_cChipId',`16#$cChipId#,16')\n");
  print MYFILE ("define(`m4_cSubVersId',`16#$cSubVersId#,16')\n");
  print MYFILE ("define(`m4_$projectdir',`1')\n");
  print MYFILE ("define(`m4_$ivariant_name',`1')\n");
  print MYFILE ("define(`m4_rtl',`rtl2')\n");
  if(my $output1 = `test.bat`){
        print("\n succesfully executed\n");    
 } 

chdir("$target_dirsynth1");
######################################################################
+##############################################
#added on 13/5/2016
opendir( my $synthdir,$target_dirsynth1) or die "Couldn't enter config
+ directory: $!\n";
          print("\nSYNTHESIS INPUT FILES IN CURRENT DIRECTORY \n");
          my $synthfilelist = glob "*.qsf";
          print ("\n$synthfilelist \n");

#closedir($target_dirsynth1);

       my $originalquartus ;
       my $latestquartus ;
       my $readlineqo;
       my $readlineql ;
#print "\nENTER THE CONFIGURATION FILE NAME FROM THE ABOVE LIST \n";
#my $configfile = <STDIN>;
open (my $OFILE,$synthfilelist) || die "couldnt open file: $!";  
   while ($readlineqo = <$OFILE>) {
       chomp $readlineqo;
       if ($readlineqo =~ /ORIGINAL_QUARTUS_VERSION/) { 
       my @originalqarray = (split / +/ , $readlineqo);
       $originalquartus = $originalqarray[3];
       print "\nthe original quartus $originalquartus\n";
         }
#next if $readlineqo =~ /^ $/;
#       }
#  close($OFILE); 

#open (my $LFILE,$synthfilelist) || die "couldnt open file: $!";  
#  while ($readlineql = <$LFILE>) {
#       chomp $readlineql;
       print "into the second loop $readlineqo\n";
       if ($readlineqo =~ /LAST_QUARTUS_VERSION/) {
       my @latestqarray = (split / +/ , $readlineqo);
       $latestquartus = $latestqarray[3];
       print "\nthe latest quartus $latestquartus\n";
       }
     next if $readlineqo =~ /^ $/;
    }       
   close($OFILE); 

closedir($target_dirsynth1);
######################################################################
+##############################################
print("\n Enter y or n to continue with synthesis \n");
my $choice = <STDIN>;
chop($choice);
if ($choice eq "y") {
  system ("qcmd.bat $toplevelentity");
}
else {
    print "continue manually with synthesis\n";
}
[download]

Not very much of that code is necessary. Your later code doesn't need all that readdir stuff and the stuff reading the config file.

Note that you are printing out the current line in the line:

print "into the second loop $readlineqo\n";
[download]

So, if you are seeing the output into the second loop .., then your line consists of two dots. Maybe that is the case, but maybe you are reading the wrong file.

this code is doing many things. at first it is generating rtl file using m4 switch and values of some generic variable from config file and then its synthesizing them. what i wanted is to provide a switch for one particular version of synthesizing software and that to as per the qsf file (for which i added the portion of code that would get value about last and original quartus version.). to do so i have coded the portion inside two ###################### blocks. though the code is working it is only able to get original quartus version and not the last quartus version inspite it is printing "into the second loop $readlineqo" for that no of times as there are lines in qsf file. couldnt debug what mistake i am doing .

Hi mrityunjaynath,

Due to lack of time I have only briefly skimmed your code - and I think that many other readers would also appreciate it if you could reduce the amount of code needed to reproduce the problem, as the pages I linked to earlier explain. At first glance, it seems that the block of code inside the ##### comment markers is mostly independent of the rest of the code.

Does your script ever output "into the second loop set_global_assignment -name LAST_QUARTUS_VERSION 11.1"?

If not, then my guess is that you have more than one file with the extension .qsf in the path $target_dirsynth1 and the glob is picking the wrong one.

Regards,
-- Hauke D