Reverted NA values from 2.0 to 0.0 bbc it was causing too much difference in the…

Reverted NA values from 2.0 to 0.0 bbc it was causing too much difference in the epistatic model maps.

alphabets/mt.20.txt

-P
-G
-E
-K
-R
-Q
-D
-S
-N
-T
-H
-C
-I
-V
-W
-Y
-F
-A
-L
-M

computePred.R

@@ -50,9 +50,6 @@ if(sum(colnames(jet)=="traceMax")==1){trace=jet[,"traceMax"]}else{trace=jet[,"tr
 # compute evolutionary distances of all sequences with respect to the query
 distTrace = binAli[2:N[1],] %*% trace^2
 
-# print("Printing evolutionary distance matrix")
-# print(distTrace)
-
 wt=read.fasta(paste(prot,".fasta",sep=""))
 n = length(wt[[1]])
 wt = wt[[1]][1:n]
@@ -222,7 +219,7 @@ print(paste("Reading frequencies:"))
 for (row in 1:nrow(jet)) {
   frequencies<-append(frequencies, jet[row, "freq"] )
 }
-#print(frequencies)
+print(frequencies)
 freq_mean = mean(frequencies)
 
 #alpha = 0.6
@@ -241,7 +238,7 @@ for (row in 1:nrow(jet)) {
 #     alpha<-append(alpha, (1.0 - alpha_val))
 #   }  
 # }
-# print(alpha)
+print(alpha)
 
 
 

gemme.py

@@ -146,7 +146,7 @@ def parseGEMMEoutput(inputFile, verbose):
             if item[0] == "\"":
                 aaColumn.append(item)
             elif (item == 'NA'):
-                tempList.append(2.0000000)
+                tempList.append(0.0000000)
             else:
                 tempList.append(float(item))
         matrixData.append(tempList)

gemmeAnal.py

@@ -169,12 +169,6 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 	reCode=subprocess.call(jetcmd,shell=True)
 	if os.path.isfile(prot+"/"+prot+"_jet.res"):
 		os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
-	# # Copy the refined MSA file!
-	# if os.path.isfile(prot+"/"+prot+"_"+chainID+".fasta"):
-	# 	os.rename(prot+"/"+prot+"_"+chainID+".fasta",prot+"_"+chainID+".fasta")
-	# if os.path.isfile(prot+"/"+prot+"_"+chainID+".psiblast"):
-	# 	os.rename(prot+"/"+prot+"_"+chainID+".psiblast",prot+"_"+chainID+".psiblast")
-	
 	return(reCode)
 
 # Run Rscript to compute predictions

pred.R

@@ -350,11 +350,11 @@ computePredSimple<-function(mat, distTrace, wt, thresh){
  # matAli = convertAliToTrace(mat,trace,wt)
   # go over all positions
   for(i in 1:leSeq){
-  
     res = vector()
     for(a in aa){
       if(a!=wt[i]){
         sel = which(mat[,i]==a)
+<<<<<<< HEAD
         # print(sel)
         if(length(sel)>0){
           sortedDist=sort(distTrace[sel-1])
@@ -367,6 +367,9 @@ computePredSimple<-function(mat, distTrace, wt, thresh){
             }
           
           }
+=======
+        if(length(sel)>0){sortedDist=sort(distTrace[sel-1])}
+>>>>>>> parent of bd075e8... Added mt.20.txt, namely full alphabet!
         else{sortedDist = c()}
         res = c(res,findMinDist(sortedDist,thresh))
       }