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
You can try these links Mr. Data Converter
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 is written in node.js, and the queries return data in JSON format.