my $previous = '';
while (<>) {
  @gtf = split /\s+/, $_;
  chomp();
  # switch those two to chomp the line before you split it,       
  # otherwise your chomp is meaningless.  Also, those are  
  # the default arguments to split:
while(<>){
  chomp;
  my @gtf = split;


  if ("$gtf[9]" ne "$previous") {
  # don't put quotes around single variables; potentially buggy
  if( $gtf[9] ne $previous ){


    $gtf[2] =~ tr/ex*/ex1/;
    # this probably doesn't do what you want.  
    # tr/// transliterates characters: here e becomes e, 
    #   x becomes x, and a literal asterisk becomes 1.  
    # If you want to reset $gtf[2] back to 'ex1', just do so:
    $gtf[2] = 'ex1';


  } else {
    $gtf[2]++;
    # this may bite you too.  $x='ex9'; $x++; $x=='ey0'
    # you probably want to increment just the number:
    $gtf[2] =~ s/(\d+)/$1+1/e;
  }

  # now save $gtf[9] in $previous so it can be compared to the next line
  $previous = $gtf[9];


  # here is where you would print out the array values, or do whatever you like with them
}