open(my $master_file, '<', "file1") or die "couldn't open master";
my %valid = map { chomp; ($_ => 1) } <$master_file>;
close $master_file;
open(my $data_file, '<', "file2") or die "couldn't open data file";
while (<$data_file>) {
    my ($key) = split /\s/;
    print if $valid{$key};
}
close $data_file;
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We create a hash of good values from the masterfile, for quick lookup. Then we iterate over the lines in the data file, printing them only if the first value is a valid key.