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I need to convert GTFS (General Transit Feed Specification https://developers.google.com/transit/gtfs/reference), data into some GIS data format like ESRI Shapefile or KML or something else.

Do you know any tool for this issue?

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There's a tool that goes from GTFS to KML:

http://code.google.com/p/googletransitdatafeed/wiki/KMLWriter

and a KML to shape file tool at

http://sourceforge.net/projects/pygearth/

For more details please click here

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Bob Heitzman's XLS for GTFS spreadsheet tools can import and export KML, as well as its main function to import and export GTFS feed.

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ArcGIS Pro 2.2 now provides two tools to create features (shapefile or feature classes) from GTFS data:

Converts a GTFS shapes.txt file from a GTFS public transit dataset to a polyline feature class showing the physical paths taken by vehicles in the public transit system.

Converts a GTFS stop.txt file from a GTFS public transit dataset into a feature class of public transit stops.

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I wrote a simple web-based tool for converting KML files into GTFS shapes.txt files at:

http://bdferris.github.io/kml-to-gtfs-shapes/

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