#!/usr/bin/env python

#### INSTRUCTIONS FOR USE:
# call program as follows: ./pstemp.py <MOTLEN> <DATAFILE> <CONSFILE>
# 				e.g. ./ps1temp.py 6 allinter allintercons
# make sure the pstemp.py is marked as executable: chmod +x pstemp.py
# or in windows with:       python ps1temp.py 6 allinter allintercons
# once you have put python in your path

import sys

mlen = int(sys.argv[1])
datafile = sys.argv[2]
consfile = sys.argv[3]

alphabet = ['A', 'T', 'G', 'C']

def main():
	data = readdata(datafile)
	cons = readdata(consfile)

	motcount = countmotif(data)
	motcountcons = countmotifcons(data,cons)

	motcons = []

	########## YOUR CODE HERE
	# create a list motcons that fills the conservation score (motcons) of each motif
	# note: in python 3/4 = 0, therefore you should use float(3)/4







	print "Top 50 motifs:"
	printtop(motcount,50)

	print ""
	print "Top 50 motifs when considering conserved regions:"
	printtop(motcountcons,50)
	
	print ""
	print "Top 50 most conserved motifs:"
	printtop(motcons,50)

def countmotif(data):
	# function returns an array indexed by motif (see m2idx below) containing
	# counts for all motifs found in data
	
	counts = []
	for i in range(pow(4,mlen)):
		counts.insert(i,0)

	########## YOUR CODE HERE
	# write code to fill counts: the count for each motif. notice that counts is 
	# indexed by the motif number
	# you will want to look up how to perform substrings. you will need to use
	# m2idx to produce your indexes









	return counts

def countmotifcons(data,cons):
	# like countmotif below but only counts a motif if all positions are marked with
	# *'s in cons.

	counts = []
	for i in range(pow(4,mlen)):
		counts.insert(i,0)
	
	########## YOUR CODE HERE
	# fill in code to do the same as countmotif except to only count motifs where
	# all positions are conserved







	return counts

def printtop(count,numprint):
	motcount = [(count[i], idx2m(i)) for i in range(len(count))]
	motcount.sort()
	motcount.reverse()
	for i in range(numprint):
		print motcount[i]

def m2idx(motif):
	# maps a dna motif to a unique index number
	# returns -1 if motif contains characters not in alphabet
	
	idx=0
	try:
		for i in range(len(motif)):
			idx = (idx << 2) + alphabet.index(motif[i])
	except:
		return -1

	return idx
		
def idx2m(idx):
	# maps an index to a unique motif
	motif=""
	for i in range(mlen):
		motif = alphabet[idx % 4] + motif
		idx = idx >> 2
	return motif

def readdata(file):
	f = open(file,'r')
	data = f.read()
	f.close()
	return data

main()