Few days back I wanted AGP file too. Then I came across this script at Github.

Edit: Here is my agp file:

Chr 1       108932  234     W       contig_235      1       108932  +
Chr 108933  190826  235     N       81894   fragment        yes

I am using same script. But the output file is throwing the error while uploading. Your sequence header contains 9 columns?? if yes please post an example