Changed SGEMME_PATH to ESGEMME_PATH

computePred.R

@@ -6,13 +6,13 @@
 # Usage: Rscript --save computePred.R XXXX
 
 library("seqinr")
-source(paste(Sys.getenv("SGEMME_PATH"),"/pred.R",sep=""))
+source(paste(Sys.getenv("ESGEMME_PATH"),"/pred.R",sep=""))
 
 # amino acid full alphabet
 aa = c("a","c","d","e","f","g","h","i","k","l","m","n","p","q","r","s","t","v","w","y")
 
 # BLOSUM62  matrix
-blosum62p = as.matrix(read.table(paste0(Sys.getenv("SGEMME_PATH"),"/blosum62p.txt"),row.names=1))
+blosum62p = as.matrix(read.table(paste0(Sys.getenv("ESGEMME_PATH"),"/blosum62p.txt"),row.names=1))
 bgp = blosum62p[order(rownames(blosum62p)),order(colnames(blosum62p))]
 bg = apply(bgp,1,sum)
 

sgemme.py → esgemme.py

@@ -141,7 +141,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 	chainID = chains[0]
 	
 	#TODO: Remove Bash dependency here. Make the copying process in Python
-	subprocess.call("cp $SGEMME_PATH/default.conf .",shell=True)
+	subprocess.call("cp $ESGEMME_PATH/default.conf .",shell=True)
 
 	if retMet=="input":
 		if bFile!='':
@@ -236,11 +236,11 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 # Run Rscript to compute predictions
 def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
     if (mutFile!=''):
-	    rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
+	    rcmd="Rscript --save $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
     
     #TODO: remember that there is a problem here!!!! 
     else:
-        rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
+        rcmd="Rscript --save $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
 
     print("\nRunning: \n"+rcmd)
     reCode=subprocess.call(rcmd,shell=True)

pred.R

@@ -174,7 +174,7 @@ computePSSM2<-function(mat){
 }
 
 computeNbSeqsAlph<-function(nbSeqs,alphabet){
-	path=paste(Sys.getenv("SGEMME_PATH"),"/alphabets/",sep="")
+	path=paste(Sys.getenv("ESGEMME_PATH"),"/alphabets/",sep="")
         AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
         facAA = rep(NA,20)
         for(Let in AA){
@@ -210,7 +210,7 @@ readMut<-function(fname){
 }
 
 which.class<-function(a,alphabet){
-        path=paste(Sys.getenv("SGEMME_PATH"),"/alphabets/",sep="")
+        path=paste(Sys.getenv("ESGEMME_PATH"),"/alphabets/",sep="")
         AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
         for(Let in AA){
                 Let = toString(Let)