# https://www.perlmonks.org/?node_id=11110379
# usage: perl search_db.pl > Outfile.txt

use strict;
use warnings;
use KyotoCabinet;

# construct the database object
my $db = KyotoCabinet::DB->new();

# open the database
if (! $db->open('db.kch#msiz=128m', $db->OREADER | $db->ONOLOCK)) {
    die "open error (db): ", $db->error;
}
my $cur = $db->cursor;

open my $fh, '<', 'peptides.txt' or die "open error: $!\n";

while ( my $pep = <$fh> ) {
    my $ids = ''; chomp $pep;

    $cur->jump; # first record
    while ( my ($key, $val) = $cur->get(1) ) {
        $ids .= ",$key" if index($val, $pep) >= 0;
    }

    print "$pep\t", substr($ids, 1), "\n" if $ids;
}

close $fh;

$cur->disable;
$db->close;