If I may, I'd like to offer just a few suggestions which may assist your efforts:

• In case you haven't, always use strict; use warnings; at the top of your scripts
• Use the three-argument form of open
• Use split to get the ID from the file's lines
• Build a hash from @isos20 and use that to check for an ID match when reading the file

Give the above items, consider the following refactoring:

use strict;
use warnings;

my $posfile = 'posfile.txt';
my $pos_two = 'pos_two.txt';
my @isos20  = qw/these are the array elements/;
my %isos20  = map { $_ => 1 } @isos20;

#open file to write filtered lines to
open my $OUT2, '>', $pos_two or die "cannot open $pos_two: $!";

#open file to filter
open my $IN2, '<', $posfile or die "cannot open $posfile: $!";

while (<$IN2>) {
    my $comp = ( split /,/ )[0];
    print $OUT2 $_ if $isos20{$comp};
}

close $IN2;
close $OUT2;
[download]

Notice that there are fewer instructions within the while loop. Instead of assigning the value of Perl's default scalar $_ to $line, just operate on $_.

The split gets the ID from the file's string by creating a list of string elements and taking the zeroth element of that list. The $isos20{$comp} notation 'looks' for that ID within the hash (constructed using map above), and prints the line to the output file if it's in the hash.

Why use a hash instead of grepping the array for a match? Using a hash is a much faster, more efficient way of detecting a match, in this case. For each line, the entire array is traversed by grep to find a possible match. However, a hash has a very efficient look-up algorithm, so will work better--significantly so, if the array is quite large.

Hope this helps!

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