Corrected column names in full raw escott output.

Column names in raw escott full single point mutational files
(such as BLAT_normPred_evolCombi.txt,
BLAT_normPred_evolEpi.txt and BLAT_normPred_evolInd.txt)
were V1 V2.....Vn, where n is number of residues in the protein.
I replaced those V letters with correct single amino acid
identifiers.

prescott/computePred.R

 # Copyright (c) 2018: Elodie Laine
 # Copyright (c) 2022-2023: Mustafa Tekpinar
-# This code is part of the gemme package and governed by its license.
+# This code is part of the prescott package and governed by its license.
 # Please see the LICENSE.txt file included as part of this package.
 
 # Usage: Rscript --save computePred.R XXXX
@@ -140,7 +140,23 @@ print(trace)
 distTrace = binAli[2:N[1],] %*% trace^2
 
 wt=read.fasta(paste(prot,".fasta",sep=""))
+
 n = length(wt[[1]])
+# # print(wt)
+# for ( residue in wt){ 
+#   print(toupper(residue))
+# }
+# print(length(wt[[1]]))
+myWTSequence <- wt[[1]]
+#create empty list of length  of the wt sequence
+myColumnNames <- vector(mode='list', length=length(wt[[1]]))
+# myColumnNames <- list()
+for ( k in 1:length(wt[[1]])) {
+  # print(toupper())
+  myColumnNames[[k]] <-paste(toupper(myWTSequence[k]), k, sep = "")
+}
+# print(myColumnNames)
+
 wt = wt[[1]][1:n]
 #indicesQ = getIndicesAli(ali$seq,1)
 
@@ -191,10 +207,10 @@ if(simple){
   normPred=normalizePred(pred, trace, wt)
   rownames(normPred)=aa
   # output the normalized predicted mutational effects based on sequence counts (conservation at the bottom)
-  write.table(normPredInd,paste0(prot,"_normPred_evolInd.txt"))
+  write.table(normPredInd,paste0(prot,"_normPred_evolInd.txt"), col.names=myColumnNames)
 
   # output the predicted normalized mutational effects based on evolutionary distance (conservation at the bottom)
-  write.table(normPred,paste0(prot,"_normPred_evolEpi.txt"))
+  write.table(normPred,paste0(prot,"_normPred_evolEpi.txt"), col.names=myColumnNames)
 }else{
   #Independent model normalization
   normPredInd = normalizePredWithNbSeqsZeroSelMult(predInd, trace, wt, list(pos,subsaa))
@@ -247,7 +263,7 @@ if(simple){
   normPredCombi = normalizePredWithNbSeqsPC(pred,trace,wt,alpha,nbSeqs,alphabet)
   rownames(normPredCombi)=aa
   # output the predicted mutational effects based on sequence counts (conservation at the bottom)
-  write.table(normPredCombi,paste0(prot,"_normPred_evolCombi.txt"))
+  write.table(normPredCombi,paste0(prot,"_normPred_evolCombi.txt"), col.names=myColumnNames)
 }else{
   #normPredCombi = normalizePredWithNbSeqsPCSelMult(pred,trace,wt,list(pos,subsaa),alpha,nbSeqs[[1]],alphabet)
   normPredCombi = normalizePredWithNbSeqsPCSelMult(pred,trace,wt,list(pos,subsaa),alpha,nbSeqs,alphabet)