Google announced a new application, a Python script, that lets you download all your search queries available from Google Webmaster Tools.
Google is offering this for two reasons:
(1) They don’t have the ability to download search query data via the Google Webmaster Tools API – yet.
(2) They removed about 10% or so of the search queries that show in your analytics when moving to SSL search and that will just get worse over time.
For more details on how this script works, see the Google Webmaster blog.
Google’s John Mueller said on Google+:
Forum discussion at Google+.