gistfile1.txt

data=open("features.bed").readlines()

dict={}

for i in range(1,len(data)):
	col=data[i].strip().split()
	chr=col[0]
	start=col[1]
	stop=col[2]
	for j in range(int(start),int(stop)+1):
		if j in dict:
			dict[j]+=1
		else:
			dict[j]=1
	print str(chr)+":"+str(start)+"-"+str(stop)+" counted."

out=open("features.depth","w")

for key in range(min(dict.keys())/5000*5000+5000,max(dict.keys())+1,5000):
	print >> out, str(key) +"\t"+ str(dict[key])

out.close()