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I combined two shapefiles and noticed that the polygons didn't overlay perfectly. How can I resolve these intersections to snap to their closest neighbours?

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This is a closer look at the intersections: enter image description here

I brought these files together using mysql, however I've been using ogr2ogr and python also.

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You have two polygons overlapping. They both represent the same area/district . When you merge the two layer there is a difference in the shape of the 2 polygons . This is most probably due to the fact that they have been generated by 2 different people. I suggest that before you merge the 2 shapefiles that you remove one polygon the one that you do not want form the original file then merge the two.

The easiest way would be to use a Desktop GIS Software like QGIS then merge the two. Unless if you require to do this automatically or programmatically then it would be more tedious to achieve.

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