Fast alternative to grep -f

If you want a pure Perl option, read your query file keys into a hash table, then check standard input against those keys:

#!/usr/bin/env perl
use strict;
use warnings;

# build hash table of keys
my $keyring;
open KEYS, "< file.contain.query.txt";
while (<KEYS>) {
    chomp $_;
    $keyring->{$_} = 1;
}
close KEYS;

# look up key from each line of standard input
while (<STDIN>) {
    chomp $_;
    my ($key, $value) = split("\t", $_); # assuming search file is tab-delimited; replace delimiter as needed
    if (defined $keyring->{$key}) { print "$_\n"; }
}

You'd use it like so:

lookup.pl < file.to.search.txt

A hash table can take a fair amount of memory, but searches are much faster (hash table lookups are in constant time), which is handy since you have 10-fold more keys to lookup than to store.

If the files are already sorted:

join file1 file2

if not:

join <(sort file1) <(sort file2)

This Perl code may helps you:

use strict;
open my $file1, "<", "file.contain.query.txt" or die $!;
open my $file2, "<", "file.to.search.in.txt" or die $!;

my %KEYS = ();
# Hash %KEYS marks the filtered keys by "file.contain.query.txt" file

while(my $line=<$file1>) {
    chomp $line;
    $KEYS{$line} = 1;
}

while(my $line=<$file2>) {
    if( $line =~ /(\w+)\s+(\d+)/ ) {
        print "$1 $2\n" if $KEYS{$1};
    }
}

close $file1;
close $file2;

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