Added mt.20.txt, namely full alphabet!

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

@@ -50,6 +50,9 @@ 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]
@@ -219,7 +222,7 @@ 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
@@ -238,7 +241,7 @@ for (row in 1:nrow(jet)) {
 #     alpha<-append(alpha, (1.0 - alpha_val))
 #   }  
 # }
-print(alpha)
+# print(alpha)
 
 
 

gemme.py

@@ -512,7 +512,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             print("       Can not generate "+prot+"_normPred_evolCombi.png file!")
         print("done")
 
-    cleanTheMess(prot,bFile,fFile, chainID=chains[0])
+    #cleanTheMess(prot,bFile,fFile, chainID=chains[0])
 
 
 def main():

gemmeAnal.py

@@ -169,6 +169,12 @@ 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 +350,23 @@ 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)
-        if(length(sel)>0){sortedDist=sort(distTrace[sel-1])}
+        # print(sel)
+        if(length(sel)>0){
+          sortedDist=sort(distTrace[sel-1])
+
+          if((i==694) & (a=="v")) {
+            print(i)
+            print(sel)
+            #print(distTrace[sel-1])
+            print(sortedDist)
+            }
+          
+          }
         else{sortedDist = c()}
         res = c(res,findMinDist(sortedDist,thresh))
       }