my $flag = 0 ;
my $scaffold ;
my $enumerator ;

while (my $fastaline=<FILE>) {
  if ($fastaline=~ m/^>(\S*)/) {
    $scaffold   = $1 ;
    $enumerator = 1 ;
    $flag       = 1 ;
  }
  elsif ($fastaline =~ m/[ACGT]/) {
    if ($flag) {
      print WORKFILE ">$scaffold.$enumerator\n" ;
      $enumerator++ ;
      $flag = 0 ;
    } ;  
    print WORKFILE $fastaline ;
  }
  else {
    $flag = 1 ;
  } ;
} ;