Changed default.conf file copy process from bash to more Pythonic way.

esgemme.py

@@ -173,7 +173,11 @@ 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 $ESGEMME_PATH/default.conf .",shell=True)
+	#subprocess.call("cp $ESGEMME_PATH/default.conf .",shell=True)
+    esgemme_path = os.path.expandvars ('$ESGEMME_PATH')
+
+    shutil.copy2(os.path.join(esgemme_path, "default.conf"), os.getcwd())
+    
 
     if retMet=="input":
         if bFile!='':
@@ -186,6 +190,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
                 shutil.copy2(bFile+".orig ", prot+"_"+chainID+".psiblast")
             else:
                 shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast")
+
             if(pdbfile == None):
                 jetcmd = "java -Xmx4096m -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+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out"