--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/profilegenerator.py	Fri Oct 03 20:54:30 2014 -0400
@@ -0,0 +1,66 @@
+import collections
+import itertools
+import sys
+
+filename=sys.argv[1]
+MOTIF=sys.argv[2]
+MOTIFSIZE=len(MOTIF)
+MaxDEPTH=int(sys.argv[3])
+MINIMUMPROB=float(sys.argv[4])##1.0/(10**4)
+MININUMCOUNT=1
+fd=open(filename)
+lines=fd.readlines()
+countbymajorallele=collections.defaultdict(list)
+for line in lines:
+    temp=line.strip().split('\t')
+    t_major=int(temp[0])
+    t_count=int(temp[2])
+    countbymajorallele[t_major].append(t_count)
+fd.close()
+sumbymajorallele=collections.defaultdict(int)
+for t_majorallele in countbymajorallele.keys():
+    sumbymajorallele[t_majorallele]=sum(countbymajorallele[t_majorallele])
+
+fd=open(filename)
+##fd=open('PCRinclude.mono.A.bymajorallele')
+lines=fd.readlines()
+allmajor=collections.defaultdict(list)
+for line in lines:
+    temp=line.strip().split()
+    if int(temp[0])%MOTIFSIZE==0:
+        if (int(temp[2])/(sumbymajorallele[int(temp[0])]*1.0))>=MINIMUMPROB:
+            if int(temp[2])>=MININUMCOUNT:
+                allmajor[int(temp[0])].append(int(temp[1]))
+##print allmajor
+allkey=allmajor.keys()
+allkey.sort()
+#print allkey
+keycount=0
+combinelist_collection=[]
+for dummycount in range(len(allkey)-1):
+    pair1,pair2=allkey[keycount],allkey[keycount+1]
+    pair1list=allmajor[pair1]
+    pair2list=allmajor[pair2]
+    #print pair1list,pair2list
+    pair1list.extend(pair2list)
+    combinelist=list(set(pair1list))
+    combinelist.sort()
+    ##print combinelist
+    combinelist_collection.append(tuple(combinelist))
+    keycount+=1
+combinelist_collection=list(set(combinelist_collection))
+newcombinelist_collection=combinelist_collection[:]
+#combinelist_collection=set(combinelist_collection)
+for smallset1 in combinelist_collection:
+    for smallset2 in combinelist_collection:
+        if set(smallset1).issubset(set(smallset2)) and smallset1 != smallset2:
+            newcombinelist_collection.remove(smallset1)
+            break
+##print combinelist_collection
+    
+for depth in range(2,MaxDEPTH+1):
+    for member_list in newcombinelist_collection:
+        for member in itertools.combinations_with_replacement(member_list,depth):
+            print 'chr'+'\t'+','.join(map(str,member))+'\t'+MOTIF
+                
+