Commit aabe1568 by Mustafa Tekpinar

Changed SGEMME_PATH to ESGEMME_PATH

parent e7a02f1e
......@@ -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)
......
......@@ -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 $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
print("\nRunning: \n"+rcmd)
reCode=subprocess.call(rcmd,shell=True)
......
......@@ -174,7 +174,7 @@ computePSSM2<-function(mat){
}
computeNbSeqsAlph<-function(nbSeqs,alphabet){
path=paste(Sys.getenv("SGEMME_PATH"),"/alphabets/",sep="")
path=paste(Sys.getenv("ESGEMME_PATH"),"/alphabets/",sep="")
AA = read.table(paste(path,alphabet,".txt",sep=""))$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)
......
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