Changed the argument --isjet2off to --jetfile.

example/example-gemme-script.sh

@@ -17,7 +17,7 @@ then
     echo "Running GEMME with a user-provided alignment file."
     echo "Using a previously produced prot_jet.res file to check reproducibility!"
     cp ../tests/BLAT_jet.res .
-    python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --isjet2on false
+    python $GEMME_PATH/gemme.py aliBLAT.fasta -r input -f aliBLAT.fasta --jetfile BLAT_jet.res
     
 else
     echo "Running GEMME with a user-provided alignment file."

gemme.py

@@ -256,9 +256,9 @@ def parse_command_line():
         default=''
     )
 
-    retMet_args.add_argument('--isjet2on', dest='isjet2on', type=str, \
-        help="If false, it will skip JET2 calculation and use a precalculated JET2 file. Default is true",
-        required=False, default="True")
+    retMet_args.add_argument('--jetfile', dest='jetfile', type=str, \
+        help="If a jet file is provided, it will skip JET2 calculation and use the precalculated JET2 data in that file. Default is None",
+        required=False, default=None)
     
     retMet_args.add_argument('--normweightmode', dest='normweightmode', type=str, \
         help="It can be one of these: 'trace', 'trace+pc', 'trace+cv' or 'trace+pc+cv'. Default is 'trace'.",
@@ -277,11 +277,11 @@ def parse_command_line():
     return args
 
 
-def doit(inAli,mutFile,retMet,bFile,fFile,n,N, isjet2on, normWeightMode):
+def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, normWeightMode):
     """
     Perfect explanation for a function: typing the function call exactly!
     doit is basically the main function in disguise!
-    doit(args.input,args.mutations,args.retrievingMethod,args.blastFile,args.fastaFile, args.isjet2on)
+    doit(args.input,args.mutations,args.retrievingMethod,args.blastFile,args.fastaFile, args.jetfile)
     """
     simple = True
 
@@ -291,19 +291,24 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, isjet2on, normWeightMode):
  
     print("query protein: "+prot)
     
-    if((isjet2on.lower()) == "true"):
+    if((jetfile) == None):
         #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!
         print("computing conservation levels...")
         launchJET(prot,retMet,bFile,fFile,n,N,nl)
         print("done")
-    elif((isjet2on.lower()) == "false"):
-        print("using previously calculated JET2 conservation levels...")
-        print("done")
     else:
-        print("ERROR: You can only use true or false after --isjet2on!")
-        sys.exit(-1)
+        print("using previously calculated JET2 data from "+jetfile+"...")
+        
+        #Doing this copy operation just due to a peculiar behaviour of JET2.
+        #According to JET2, all input files must have the same name obtained 
+        #from the fasta file right after the > symbol.
+        #Weird but true!
+        if(jetfile!=prot+"_jet.res"):
+            shutil.copy2(jetfile, prot+"_jet.res")
+        print("done")
+
     launchPred(prot,inAli,mutFile, normWeightMode)
 
     #Do Python plotting here
@@ -350,7 +355,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, isjet2on, normWeightMode):
 def main():
     args = parse_command_line()
     doit(args.input,args.mutations,args.retrievingMethod,args.blastFile,\
-         args.fastaFile,args.nIter,args.NSeqs, args.isjet2on, args.normweightmode)
+         args.fastaFile,args.nIter,args.NSeqs, args.jetfile, args.normweightmode)
 
 if (__name__ == '__main__'):
     main()