Commit e9dcd04c by Mustafa Tekpinar

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.
parent 606b4597
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......@@ -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)
......
......@@ -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)
......
......@@ -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
......
......@@ -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))
}
......
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