import re
import sys
import random
import string
import operator
import copy


def main():

	number_of_randomizations = int(sys.argv[1])

	ORIGIN = open("/mnt/wigstore3/user/kendall/stillman05/wthu.sc3.replication.origins.txt", "r")
	CHROMINFO = open("/mnt/wigstore3/user/kendall/stillman04/sc3.chromInfo.txt", "r")

	roman = {'1': "I", '2': "II", '3': "III", '4': "IV", '5': "V", '6': "VI", '7': "VII", '8': "VIII", '9': "IX", '10': "X", '11': "XI", '12': "XII", '13': "XIII", '14': "XIV", '15': "XV", '16': "XVI"}

	chrominfo = dict()
	for x in CHROMINFO:
		arow = x.rstrip().split("\t")
		thisChrom = arow[0]
		thisChromLength = int(arow[1])
		chrominfo[thisChrom] = thisChromLength


	origin = dict()
	x = ORIGIN.readline()
	for x in ORIGIN:
		arow = x.rstrip().split("\t")
		thisChromNumber = arow[0]
		thisStart = arow[1]
		thisEnd = arow[2]
		thisStatus = arow[5]

# This widden the range of origin chromosome locus to check - up to BOTH upstream and downstream 4750bp. Making the total range maybe around 10kb to count reads.
# From the previous EdU pulldown data, under HU45 or HU90 condition, WT strain has early origin peaks ranging from around 5kb to 15kb. However, the confirmed origin range from OriDB only has around maybe 250bp. Therefore, the idea is to widden the range and count the reads that in the range.
		rangeStart = int(thisStart) - 4750
		rangeEnd = int(thisEnd) + 4750

		if rangeStart < 1:
			rangeStart = 1
		else:
			pass

		if rangeEnd > int(chrominfo[thisChrom]):
			rangeEnd = int(chrominfo[thisChrom])
		else:
			pass

		#if thisStatus == "Confirmed":
		#	pass
		#else:
		#	continue

		thisChrom = "XXX"
		if roman.has_key(thisChromNumber):
			thisChrom = "chr" + roman[thisChromNumber]

		if thisChrom == "XXX":
			continue

		#####  We're going to pretend chrXII:430000-500000 doesn't exist for origins and for reads.
		if thisChrom == "chrXII":
			if rangeStart >= 430000 or rangeStart <= 500000:
				continue
			if rangeEnd >= 430000 or rangeEnd <= 500000:
				continue
		#####  End of code passing over this region on chrXII


		if origin.has_key(thisChrom):
			pass
		else:
			origin[thisChrom] = []
		origin[thisChrom].append([thisChrom, int(rangeStart), int(rangeEnd)])


	randomOriginList = []
	for i in range(number_of_randomizations):
		randomOrigin = dict()
		for thisChrom in origin.keys():
			for v in origin[thisChrom]:
				thisLength = v[2] - v[1]
				randomStart = random.randint(1, int(chrominfo[thisChrom]) - thisLength)
				if v[0] == "chrXII":
					#excludeStart = 450000 - thisLength
					#excludeEnd = 490500
					excludeStart = 430000
					excludeEnd = 500000
					while True:
						if randomStart >= excludeStart and randomStart <= excludeEnd:
							randomStart = random.randint(1, int(chrominfo[thisChrom]) - thisLength)
						else:
							break
					#  This code below might create a new randomStart in the exclude region
					#  Have to keep trying until outside exclude region
					#exclude = range(450000 - thisLength,490500)
					#if randomStart in exclude:
					#	randomStart = random.randint(1, int(chrominfo[thisChrom]) - thisLength)
					#else:
					#	pass
				else:
					pass

				if randomOrigin.has_key(thisChrom):
					pass
				else:
					randomOrigin[thisChrom] = []
				randomOrigin[thisChrom].append([thisChrom, randomStart, randomStart + thisLength])
		randomOriginList.append(copy.deepcopy(randomOrigin))


	totalReads = []
	for i in range(number_of_randomizations + 1):
		totalReads.append(0)

	for x in sys.stdin:
		arow = x.rstrip().split("\t")
		thisChrom = arow[0]
		thisPosStart = int(arow[1])
		thisPosEnd = int(arow[2])

		if origin.has_key(thisChrom):
			pass
		else:
			continue

		if chrominfo.has_key(thisChrom):
			pass
		else:
			continue
			
		#####  We're going to pretend chrXII:430000-500000 doesn't exist for origins and for reads.
		if thisChrom == "chrXII":
			if thisPosStart >= 430000 or thisPosStart <= 500000:
				continue
			if thisPosEnd >= 430000 or thisPosEnd <= 500000:
				continue
		#####  End of code passing over this region on chrXII
			

		for r in origin[thisChrom]:
			if thisPosStart >= r[1] and thisPosStart <= r[2]:
				totalReads[0] += 1
			else:
				if thisPosEnd >= r[1] and thisPosEnd <= r[2]:
					totalReads[0] += 1
				else:
					continue

		for i in range(1, number_of_randomizations + 1):
			for r in randomOriginList[i - 1][thisChrom]:
				if thisPosStart >= r[1] and thisPosStart <= r[2]:
					totalReads[i] += 1
				else:
					if thisPosEnd >= r[1] and thisPosEnd <= r[2]:
						totalReads[i] += 1
					else:
						continue

	realCount = totalReads[0]
	higherThanRealCount = 0

	for i in range(number_of_randomizations + 1):
		if i > 0:
			if totalReads[i] > realCount:
				higherThanRealCount += 1
		print totalReads[i]

	print
	print realCount, higherThanRealCount

if __name__ == "__main__":
	main()