#!/user/bin/python
import sys

out=open(sys.argv[1],'w')


DIC_TINAT={}

with open("DAC.SB_Mean_responsive_TSSs.csv.LTR12C.cor",'r') as fin1:
	for line in fin1:
		str=line.strip().split("\t")
		if str[0] not in DIC_TINAT.keys():
			DIC_TINAT[str[0]]=[]
			for i in range(int(str[1]),int(str[2])+1):
				DIC_TINAT[str[0]].append(i)
		else:
			for i in range(int(str[1]),int(str[2])+1):
				DIC_TINAT[str[0]].append(i)
	#print DIC_TINAT
fin1.close()

         

#transfer the TCGA to num
DIC_align={}
linenum=[]

input= [line.rstrip() for line in open('test.muscle')]

for i in range(0,len(input)):
	if input[i].startswith(">"):
		#print input[i]
		linenum.append(i)

for i in range(len(linenum)):
	DIC_align[input[linenum[i]].split(">")[1]]=''.join(input[(linenum[0]+1):(linenum[1])])
#print DIC_align

for i in range(len(DIC_align)):
#for i in range(2):
	print i
	chr_str_end = DIC_align.keys()[i]
	#print DIC_align.keys()[i]
	#print chr_str_end
	sequence = DIC_align.keys()[i]
	chr=chr_str_end.split(":")[0]
	plotnum=[]
	cornum=[]
	if chr.startswith("LTR12C"):
		start_count=0
		for l in DIC_align.values()[i]:
			if l =="-":
				start_count += 0
					#print start_count
				plotnum.append(start_count)
				#print cornum						
				cornum.append('0')
				#print plotnum
			else:
				start_count += 1
				#print start_count
				plotnum.append(start_count)
				cornum.append('0')
	else:
		str=int(chr_str_end.split(":")[1].split("-")[0])
		end=int(chr_str_end.split(":")[1].split("-")[1].split("(")[0])
		strand=chr_str_end.split("(")[1].split(")")[0]
		if strand == "+":
			start_count=str
			#print DIC_align.values()
			#print DIC_align.values()[i]
			for l in DIC_align.values()[i]:
				#print l
				if l =="-":
					start_count += 0
					#print start_count
					cornum.append(start_count)
					#print cornum						
					plotnum.append('0')
					#print plotnum
				else:
					start_count += 1
					#print start_count
					cornum.append(start_count)
					if start_count in DIC_TINAT[chr]:
						plotnum.append('1')
					else:
						plotnum.append('0')
		else:
			start_count=end
			for l in DIC_align.values()[i]:
				if l =="-":
					start_count -= 0
					cornum.append(start_count)
					plotnum.append('0')
				else:
					start_count -= 1
					cornum.append(start_count)
					if start_count in DIC_TINAT[chr]:
						plotnum.append('1')
					else:
						plotnum.append('0')
	print >> out, '%s\t%s\t%s\t%s'%(chr_str_end,DIC_align.values()[i],''.join(plotnum),(cornum))