def main(k,inter,con):
    # this makes everything happen
    # k is the length of the motif
    # intergenic is a string with the name ofthe intergenic file

    # METHOD 1
    intergenic = read_data(inter)
    count      = exhaustive(k,intergenic)
    
    # METHOD 2
    con        = read_data(con)
    count2     = exhaustivec(k,intergenic,con)
    
    # METHOD 3
    count2     = exhaustiveone(k,intergenic)


    

def enummotif(k, alphabet):
    #enummotif exhaustively enummerates all motifs of length k
    #alphabet is a list of letters in the alphabet
    size = len(alphabet)
    ra   = range(size)
    pm   = alphabet
    #pm is premotif
    rk   = range(k-1)
    #because the alphabet itself counts
    pm2  = []
    
    for i in rk:
        rpm = range(len(pm))
        for j in rpm:
            for k in ra:
                #print k
                pm2[:0]=[pm[j]+alphabet[k]]
                #print pm2
                #print pm
        pm=[]
        pm[:0]=pm2
        pm2=[]

    return pm

profile_ambiguities = {'A': 'A', 'C': 'C', 'G':'G', 'T':'T',
                       'S':'CG','W':'AT','R':'AG','Y':'CT','M':'AC','K':'TG',
                       'B':'TCG','D':'ATG','H':'ATC','V':'ACG','N':'ATCG'}

def profile2seqs(profile):
    # creates all the instances of a motif that are possible,
    # expanding Y into CT etc
    list = []
    if not profile:
        return ['']
    for rest in profile2seqs(profile[:-1]):
        for first in map(None, profile_ambiguities[profile[-1]]):
            list.append(rest+first)
    return list

def read_data(file):
    f=open(file,'r')
    t=f.read().replace('-','')
    return t


    
def exhaustive(k, intergenic):
    # scans the intergenic genome counting all k-mers
    # intergenic is the string to be parsed (read with read_data)
    # k is the length of the profile
    # written by Reina Riemann Spring05 6.096

    alphabet = ['C','G','T','A']
    kmer = enummotif(k, alphabet)
    count=[]
    for i in range(len(kmer)):

        #PROVIDE YOUR CODE HERE



       
    final=[(count[i],kmer[i]) for i in range(len(kmer))]
    final.sort()
    print final 
    return final
        
def exhaustivec(k, intergenic,con):
    # enumerates all k-mers, scans the intergenic genome 
    # intergenic is the string to be parsed (read with read_data)
    # k is the length of the profile
    # con is the string with the conservation information
    # written by Reina Riemann Spring05 6.096
    
    alphabet = ['C','G','T','A']
    kmer = enummotif(k, alphabet)
    count=[]
    stars=k*'*'
    for i in range(len(kmer)):
        count.append(0)
        
        #PROVIDE YOUR CODE HERE

    final=[(count[i],kmer[i]) for i in range(len(kmer))]
    final.sort()
    print final 
    return final


def exhaustiveone(k, intergenic):
    # exhaustive scans the intergenic genome counting all k-mers
    # intergenic is the string to be parsed (read with read_data)
    # k is the length of the profile
    # con is the string with the conservation information
    # written by Reina Riemann Spring 05
    
    alphabet = ['C','G','T','A']
    motif={} #this is a dictionary
    for j in range(0, len(intergenic)-k+1):
        #PROVIDE YOUR CODE HERE

    keys= motif.keys()

    final =[(motif[keys[i]],keys[i]) for i in range(len(keys))]
    final.sort()
    print final 
    return final