Question

Given a SHP file corresponding to European countries, and...

Given defined area corresponting to France such :

West : 005° 48' W
East : 010° E
North : 051° 30' N
South : 041° N

How to get only the dots/geometries which intersects my defined area with gdal ? so my crop indeed is a real crop, which just keep the necessary geometries. Strong preference to gdal, ogr or console solutions.

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Solution

Use GDAL's ogr2ogr command-line utility. If you have a file Europe.shp which has a spatial reference with units of degrees, then use the -clipsrc option with decimal degrees to make a new shapefile:

ogr2ogr -clipsrc -5.8 41 10 51.5 France.shp Europe.shp

There is also an example at the ogr2ogr page with France used as an example.

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