Do you know any tool that provides that? I need to manipulated GTFS file but I would like to have data available in any well-known format like XML or JSON.
GTFS are Google Transit Feed Specification
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For anyone looking for something like this in 2014, take a look at brendannee/node-gtfs - GitHub
From the site's readme.md:
node-GTFS loads transit data in GTFS format from GTFS Data Exchange, unzips it and stores it to a MongoDB database and provides some methods to query for agencies, routes, stops and times. It also has spatial queries to find nearby stops, routes and agencies.
node-GTFS is written in node.js, and the queries return data in JSON format.
FME by Safe Software supports GTFS and JSON or XML output among numerous other possible output formats. http://www.safe.com/