The file1 is probably too large to remember the ids, but you haven't told us how large file2 is. I guess it's much smaller, so you could try hashing the ids from it and then reading the large file line by line and check whether the id was mentioned in file2:

#!/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]

In reply to Re: Query large tab delimited file by a list by choroba
in thread Query large tab delimited file by a list by Elninh05

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