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1 import collections
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2 import itertools
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3 import sys
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4
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5 filename=sys.argv[1]
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6 MOTIF=sys.argv[2]
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7 MOTIFSIZE=len(MOTIF)
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8 MaxDEPTH=int(sys.argv[3])
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9 MINIMUMPROB=float(sys.argv[4])##1.0/(10**4)
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10 MININUMCOUNT=1
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11 fd=open(filename)
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12 lines=fd.readlines()
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13 countbymajorallele=collections.defaultdict(list)
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14 for line in lines:
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15 temp=line.strip().split('\t')
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16 t_major=int(temp[0])
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17 t_count=int(temp[2])
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18 countbymajorallele[t_major].append(t_count)
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19 fd.close()
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20 sumbymajorallele=collections.defaultdict(int)
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21 for t_majorallele in countbymajorallele.keys():
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22 sumbymajorallele[t_majorallele]=sum(countbymajorallele[t_majorallele])
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23
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24 fd=open(filename)
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25 ##fd=open('PCRinclude.mono.A.bymajorallele')
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26 lines=fd.readlines()
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27 allmajor=collections.defaultdict(list)
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28 for line in lines:
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29 temp=line.strip().split()
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30 if int(temp[0])%MOTIFSIZE==0:
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31 if (int(temp[2])/(sumbymajorallele[int(temp[0])]*1.0))>=MINIMUMPROB:
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32 if int(temp[2])>=MININUMCOUNT:
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33 allmajor[int(temp[0])].append(int(temp[1]))
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34 ##print allmajor
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35 allkey=allmajor.keys()
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36 allkey.sort()
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37 #print allkey
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38 keycount=0
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39 combinelist_collection=[]
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40 for dummycount in range(len(allkey)-1):
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41 pair1,pair2=allkey[keycount],allkey[keycount+1]
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42 pair1list=allmajor[pair1]
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43 pair2list=allmajor[pair2]
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44 #print pair1list,pair2list
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45 pair1list.extend(pair2list)
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46 combinelist=list(set(pair1list))
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47 combinelist.sort()
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48 ##print combinelist
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49 combinelist_collection.append(tuple(combinelist))
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50 keycount+=1
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51 combinelist_collection=list(set(combinelist_collection))
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52 newcombinelist_collection=combinelist_collection[:]
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53 #combinelist_collection=set(combinelist_collection)
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54 for smallset1 in combinelist_collection:
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55 for smallset2 in combinelist_collection:
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56 if set(smallset1).issubset(set(smallset2)) and smallset1 != smallset2:
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57 newcombinelist_collection.remove(smallset1)
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58 break
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59 ##print combinelist_collection
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60
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61 for depth in range(2,MaxDEPTH+1):
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62 for member_list in newcombinelist_collection:
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63 for member in itertools.combinations_with_replacement(member_list,depth):
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64 print 'chr'+'\t'+','.join(map(str,member))+'\t'+MOTIF
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65
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66
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