you can try generating a subroutine on the fly to perform all the substitutions: 
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 = "sub { ";
for my $name (sort keys %mapper) {
  my $qname = quotemeta $name;
  my $qrepl =  quotemeta $mapper{$name};
  $sub .= "s{\b$qname\b}{$qrepl}g; ";
}
$sub .= "}";
$sub = eval $sub;
die if $@;

open(IN, "<input_file");
open(OUT, ">input_file.new");
while (<IN>) {
print "%";
     tr/A-Z/a-z/;
     $sub->();
     print OUT "$_";
}
close(IN);
clse(OUT);

[download]
this way, the regular expresions are compiled just once, and also, the inner loop and the sort are removed from the while loop.

In reply to Re: How to speed up multiple regex in a loop for a big data? by salva
in thread How to speed up multiple regex in a loop for a big data? by Anonymous Monk

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