Fast alternative to grep -f

Question

file.contain.query.txt

ENST001

ENST002

ENST003

file.to.search.in.txt

ENST001  90

ENST002  80

ENST004  50

Answer 1

If you have fixed strings, use grep -F -f. This is significantly faster than regex search.

Answer 2

If you are using perl version 5.10 or newer, you can join the 'query' terms into a regular expression with the query terms separated by the 'pipe'. (Like:ENST001|ENST002|ENST003) Perl builds a 'trie' which, like a hash, does lookups in constant time. It should run as fast as the solution using a lookup hash. Just to show another way to do this.

#!/usr/bin/perl
use strict;
use warnings;
use Inline::Files;

my $query = join "|", map {chomp; $_} <QUERY>;

while (<RAW>) {
    print if /^(?:$query)\s/;
}

__QUERY__
ENST001
ENST002
ENST003
__RAW__
ENST001  90
ENST002  80
ENST004  50