database migrator source DB (altered tables or columns) > target DB

composer.json

{
  "config": {
    "platform": {
      "php": "5.3.10"
    }
  },
  "require": {
    "doctrine/dbal": "^2.5",
    "jdorn/sql-formatter": "^1.2"
  }
}

index.php

<?php
require 'vendor/autoload.php';
use Doctrine\DBAL\DriverManager;

$source = DriverManager::getConnection(array(
    'driver'   => 'pdo_mysql',
    'host'     => 'localhost',
    'user'     => 'xxx',
    'password' => 'xxx',
    'dbname'   => 'db1',
));

// schema that needs to update its structure from $source
$target = DriverManager::getConnection(array(
    'driver'   => 'pdo_mysql',
    'host'     => 'localhost',
    'user'     => 'xxx',
    'password' => 'xxx',
    'dbname'   => 'db2',
));

// add type mappings when needed.
$sourcePlatform = $source->getDatabasePlatform();
$sourcePlatform->registerDoctrineTypeMapping('enum', 'string');

$targetPlatform = $target->getDatabasePlatform();
$targetPlatform->registerDoctrineTypeMapping('enum', 'string');

$sourceSchema = $source->getSchemaManager()->createSchema();
$targetSchema = $target->getSchemaManager()->createSchema();

$sql = $sourceSchema->getMigrateToSql($targetSchema, $targetPlatform);
array_unshift($sql, 'START TRANSACTION');
$sql[] = 'COMMIT';

foreach ($sql as $c) {
    echo SqlFormatter::format($c.';');
}