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


def main():

	ORIGIN = open("/Users/Elaine/Coding/TReSeq-test/wthu.sc3.replication.origins.txt", "r")
	CHROMINFO = open("/Users/Elaine/Coding/TReSeq-test/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

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


	randomOriginList = []
	for i in range(1000):
		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":
					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(1001):
		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

		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, 1001):
			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(1001):
		if i > 0:
			if totalReads[i] > realCount:
				higherThanRealCount += 1
		print totalReads[i]

	print
	print realCount, higherThanRealCount

if __name__ == "__main__":
	main()