overlap_coodinates.py

import pybedtools


a = pybedtools.BedTool('H3K4me1_enhancers.bed')
b = pybedtools.BedTool('H3K27ac_enhancers.bed')
c = pybedtools.BedTool('GRO-seq_filtered_peaks.bed')


d = (a+b+c)
e = (a+b-c)
f = (c-a-b)

d.saveas('All_enhancers.bed')
e.saveas('Histone_only_enhancers.bed')
f.saveas('GRO_only_enhancers.bed')