open(MAP, "<$new_name_map_file");
while (<MAP>) {
     chomp;
     tr/A-Z/a-z/;
     @map_line = split (/\t/);
     $mapper{$map_line[0]} = $map_line[1];
}
close(MAP);

my $sub = <<'EOS';
sub {
  while (<IN>) {
  print "%";
  tr/A-Z/a-z/;
EOS

for my $name (sort keys %mapper) {
  my $qname = quotemeta $name;
  my $qrepl =  quotemeta $mapper{$name};
  $sub .= "s{\b$qname\b}{$qrepl}g;\n";
}

$sub .= <<'EOS'
    print OUT $_;
  }
}
EOS

$sub = eval $sub;
die if $@;

open(IN, "<input_file");
open(OUT, ">input_file.new");
$sub->();
close(IN);
clse(OUT);