use strict;
use warnings;
use Data::Dumper;
my $file = \"a\nb\nb\nc\nc\nd\nd\nd\nf\nf\nf";  # In memory 'file'
my @ids = qw( a b c d e f g );
open my $FILE, '<', $file or die "cannot open input file";
my @lines = <$FILE>;  # Read entire file into an array
close $FILE;

my %counts;
ID:
foreach my $id (@ids) {
    my $count = grep { /$id/ } @lines;
    if ($count) {
        $counts{$id} = $count;
        next ID;
    }
    warn "$id not found\n";
}

print Dumper \%counts;
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OUTPUT:
e not found
g not found
$VAR1 = {
          'd' => 3,
          'a' => 1,
          'c' => 2,
          'f' => 3,
          'b' => 2
        };
[download]