Removed ESGEMME_PATH dependency for alphabets files.

Dockerfile

@@ -9,12 +9,13 @@ ENV ESGEMME_PATH=/home/tekpinar/research/lcqb/ESGEMME
 COPY ./JET2/ ./JET2/
 COPY ./naccess2.1.1 ./naccess2.1.1
 COPY ./ESGEMME/esgemme/esgemme.py ./ESGEMME/esgemme/esgemme.py
+COPY ./ESGEMME/esgemme/alphabets ./ESGEMME/esgemme/alphabets
 COPY ./ESGEMME/esgemme/__init__.py ./ESGEMME/esgemme/__init__.py
 COPY ./ESGEMME/setup.py ./ESGEMME/setup.py
 COPY ./ESGEMME/requirements.txt ./ESGEMME/requirements.txt
 COPY ./ESGEMME/README.md ./ESGEMME/README.md 
-COPY ./ESGEMME/pred.R ./ESGEMME/pred.R
-COPY ./ESGEMME/computePred.R ./ESGEMME/computePred.R
+COPY ./ESGEMME/esgemme/pred.R ./ESGEMME/esgemme/pred.R
+COPY ./ESGEMME/esgemme/computePred.R ./ESGEMME/esgemme/computePred.R
 COPY ./ESGEMME/esgemme/default.conf ./ESGEMME/esgemme/default.conf
 COPY ./ESGEMME/data/ ./ESGEMME/data/
 COPY ./ESGEMME/examples/ ./ESGEMME/examples/

esgemme/esgemme.py

@@ -323,6 +323,10 @@ def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
     with as_file(source) as esgemme_computePred_R_path:
         shutil.copy2(esgemme_computePred_R_path, os.getcwd())
 
+    source = files('esgemme').joinpath('alphabets/'+alphabet+'.txt')
+    with as_file(source) as esgemme_alphabet:
+        shutil.copy2(esgemme_alphabet, os.getcwd())
+        
     if (mutFile!=''):
         # rcmd="Rscript --save $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
         rcmd="Rscript --save computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet

esgemme/pred.R

@@ -174,9 +174,11 @@ computeNbSeqs<-function(mat,gap=FALSE){
 # }
 
 computeNbSeqsAlph<-function(nbSeqs,alphabet){
-	path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
-        AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
-        facAA = rep(NA,20)
+#	path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
+#        AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
+        AA = read.table(paste(alphabet,".txt",sep=""))$V1
+
+	facAA = rep(NA,20)
         for(Let in AA){
                 Let = toString(Let)
                 lets = strsplit(Let,"")[[1]]
@@ -210,8 +212,9 @@ readMut<-function(fname){
 }
 
 which.class<-function(a,alphabet){
-        path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
-        AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
+#        path=paste(Sys.getenv("ESGEMME_PATH"),"/data/alphabets/",sep="")
+#        AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
+	AA = read.table(paste(alphabet,".txt",sep=""))$V1	
         for(Let in AA){
                 Let = toString(Let)
                 lets = tolower(strsplit(Let,"")[[1]])

examples/example-esgemme-script.sh

@@ -8,6 +8,8 @@ then
     # rm -rf BLAT.pdb
     # rm -rf BLAT.fasta
     rm -rf BLAT*
+    rm -rf *.R
+    rm -rf *.txt
     rm -f default.conf caracTest.dat
     rm -rf bin*.fasta
     rm -rf ../data/blat-af2.pdb.dssp ../data/blat-af2.pdb.dssp.new

setup.py

@@ -64,5 +64,5 @@ setup(name='esgemme',
           ]
       },
       include_package_data=True,
-      package_data={'esgemme':['default.conf', 'computePred.R', 'pred.R']},
+      package_data={'esgemme':['default.conf', 'computePred.R', 'pred.R', 'alphabets/*']},
       )