<?php
// database stuff

$host = '127.0.0.1';
$db   = 'test';
$user = 'root';
$pass = '';
$charset = 'utf8';

$dsn = "mysql:host=$host;dbname=$db;charset=$charset";
$opt = [
    PDO::ATTR_ERRMODE            => PDO::ERRMODE_EXCEPTION,
    PDO::ATTR_DEFAULT_FETCH_MODE => PDO::FETCH_ASSOC,
    PDO::ATTR_EMULATE_PREPARES   => false,
];
$pdo = new PDO($dsn, $user, $pass, $opt);

$stmt = $pdo->query('SELECT html_column FROM my_table');
$dirty_html = $stmt->fetch();

// htmlpurifier stuff

require_once '/path/to/HTMLPurifier.auto.php';

$config = HTMLPurifier_Config::createDefault();
$purifier = new HTMLPurifier($config);
$clean_html = $purifier->purify($dirty_html);

// database stuff

$newstmt = $pdo->prepare('UPDATE my_table SET html_column = ?');
$newstmt->bindValue(1, $clean_html);
$newstmt->execute();