Example Drush script that does not work because site specified by alias from command line does not get bootstrapped.

vocab-test.script

#!/usr/bin/env drush

$params['vocabulary'] = drush_shift();
drush_print($params['vocabulary']);

$vid = db_query(
  "SELECT vid FROM {taxonomy_vocabulary} WHERE machine_name=:vocab", 
  array(':vocab' => $params['vocabulary'])
  )->fetchField();
drush_print($vid);