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I'm using gdaltransform to convert coordinates.

What's the best way to convert MGRS using gdaltransform given that it doesn't have an EPSG code?

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I have written a Python MGRS library to convert back and forth to lat/long, which you can then reproject as necessary.

http://pypi.python.org/pypi/mgrs

It should work in Windows in addition to your favorite unix scripting environment.

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