Some changes to make the program run on python3 (tested with 3.9.7 ).

.gitignore

 *~
 ._*
+.Rhistory
+example/.RData
+gemmeAnal.pyc
\ No newline at end of file

gemme.py

@@ -135,14 +135,14 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N):
 
     createPDB(prot,seq)
  
-    print "query protein: "+prot
-    print "computing conservation levels..."
+    print("query protein: "+prot)
+    print("computing conservation levels...")
 
     #I intend to run JET2 completely externally!!
     #It is too much buggy and it has too many dependencies. 
     #Using it with a Docker or Singularity may be the best solution!
     launchJET(prot,retMet,bFile,fFile,n,N,nl)
-    print "done"
+    print("done")
     launchPred(prot,inAli,mutFile)
     cleanTheMess(prot,bFile,fFile)
 

gemmeAnal.py

@@ -62,7 +62,6 @@ def createPDB(prot,seq):
 
 # Edit JET configuration file with correct number of Seqs & MSA
 def editConfJET(N):
-
 	reCode=subprocess.call("sed -i 's/results\t\t5000/results\t\t"+str(N)+"/' default.conf",shell=True)
 	return(reCode)
 
@@ -105,10 +104,14 @@ def launchJET(prot,retMet,bFile,fFile,n,N,nl):
 	subprocess.call("cp $GEMME_PATH/default.conf .",shell=True)
 	if retMet=="input":
 		if bFile!='':
-			subprocess.call("cp "+bFile+" "+prot+"_A.psiblast",shell=True)
+			if(bFile == prot+"_A.psiblast"):
+				shutil.copy2(bFile, bFile+".orig")
+				shutil.copy2(bFile+".orig ", prot+"_A.psiblast")
+			else:
+				shutil.copy2(bFile+" ", prot+"_A.psiblast")
 			jetcmd = "java -Xmx1000m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+prot+".pdb -o `pwd` -p J -r input -b "+prot+"_A.psiblast -d chain -n "+n+" > "+prot+".out"
 		else:
-                        print N
+			print(N)
 			editConfJET(N)
 
 			if(fFile == prot+"_A.fasta"):
@@ -139,7 +142,7 @@ def launchPred(prot,inAli,mutFile):
 	else:
 		rcmd="Rscript --save $GEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none"
 
-	print rcmd
+	print("\nRunning: \n"+rcmd)
 	reCode=subprocess.call(rcmd,shell=True)
 
 	#Add plots here with gemmemore