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

my %ids;
open my $IDS, '<', 'file2' or die $!;
while (<$IDS>) {
    chomp;
    $ids{$_} = 1;
}

open my $OUT1, '>', 'output1' or die $!;

open my $LARGE, '<', 'file1' or die $!;
my $count_matches = 0;
while (<$LARGE>) {
    my ($pos, $start, $end, $id) = split;
    ++$count_matches, print {$OUT1} $_ if $ids{$id};
}
close $OUT1 or die $!;

open my $OUT2, '>', 'output2' or die $!;
print {$OUT2} "Number_pos_1st_file\t", $LARGE->input_line_number, "\n"
+;
print {$OUT2} "Number_pos_2nd_file\t", $IDS->input_line_number, "\n";
print {$OUT2} "Nr_Matching\t", $count_matches, "\n";
print {$OUT2} "Nr_Non_matching\t",
              $IDS->input_line_number - $count_matches,
              "\n";

close $OUT2 or die $!;
[download]

($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
[download]