How does your input look like? Why slurp your whole file into an array, only to iterate later, in order to inter- change or ( do substitution ) on the array indexes. Am sure there are better ways of achieving your aim using a while loop with the open function.
You can try y/,,,/,/s like so:

  my $value='Wed,Jun,13,10:23:35,2012,,,rdy,769,busy,31,rd,0,wr,22,ka,
+6 ';
     $value=~y/,,,/,/s;

  print $value;   ## Wed,Jun,13,10:23:35,2012,rdy,769,busy,31,rd,0,wr,
+22,ka,6
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If I may suggest the following, use open function three argument, check if the open function fails and always close open file handler as soon as possible like so:

  open my $filehandler,'<',$file or die "can't open file: $!";
   # .... others codes
  close $filehandler or die "can't close file:$!";
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