--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/combinedprobforallelecombination.py	Wed Apr 01 17:05:51 2015 -0400
@@ -0,0 +1,41 @@
+import sys
+import collections
+import math
+SAMPLINGCOL=11
+ALLELE1COL=7
+ALLELE2COL=8
+SIGNCOL=4
+readprofileCOL=2
+motifCOL=3
+filaname=sys.argv[1]
+fd=open(filaname)
+lines=fd.readlines()
+binomialcombine=collections.defaultdict(list)
+for line in lines:
+    temp=line.strip().split('\t')
+    allelelist=[]
+    allelelist.append(int(temp[ALLELE1COL-1]))
+    allelelist.append(int(temp[ALLELE2COL-1]))
+    allelelist.sort()
+    #allelelist=map(str,allelelist)
+    alleleave=str(allelelist[0])+'_'+str(allelelist[1])
+    #alleleave=str(sum(allelelist)/2.0)
+    ##alleleave=str(allelelist[0])+'_'+str(allelelist[1])
+    totalcov=len(temp[readprofileCOL-1].split(','))
+    motif=temp[motifCOL-1]
+    samplingvalue=float(temp[SAMPLINGCOL-1])
+    SIGN=1 
+    binomialcombine[(totalcov,alleleave,motif)].append(SIGN*samplingvalue)
+allkeys= binomialcombine.keys()
+allkeys.sort()
+##print allkeys
+print 'read_depth'+'\t'+'allele'+'\t'+'heterozygous_prob'+'\t'+'motif'
+for key in allkeys:
+    ##templist=[str(key[0]),key[1],str(sum(binomialcombine[key])),key[2],str(map(str,(binomialcombine[key])))]
+    templist=[str(key[0]),key[1],str(sum(binomialcombine[key])),key[2]]
+
+    print '\t'.join(templist)
+#print allkeys#,binomialcombine
+    
+    
+