Retrieving upstream and downstream intron coordinates

Question

[ccag]

I have a large bed file of drosophila (dm6) coordinates of select RNA regions I am interested in. If the coordinates encompass an exon (which many of them do) I would like to return the coordinates of the 5' and 3' introns. I know there must be an easy way to do this, but I am not very familiar with RNA-seq techniques.

Eventually I'd want to integrate this into a custom script. Thanks so much!

[Asaf]

Bedtools should help