Added normweightmode as an argument to Python part of the code

computePred.R

@@ -3,7 +3,7 @@
 # This code is part of the gemme package and governed by its license.
 # Please see the LICENSE.txt file included as part of this package.
 
-# Usage: Rscript --save runPred.R XXXX
+# Usage: Rscript --save computePred.R XXXX
 
 library("seqinr")
 source(paste(Sys.getenv("GEMME_PATH"),"/pred.R",sep=""))
@@ -22,6 +22,7 @@ prot = args[1]
 aliFile = args[2]
 simple = args[3]
 fname = args[4]
+normWeightMode = args[5]
 
 # read alignment and convert to matrix
 ali=as.matrix.alignment(read.alignment(aliFile,format="fasta"))
@@ -92,7 +93,7 @@ print("running normalization...")
 #normWeightMode="trace+pc+cv"
 #normWeightMode="trace+pc"
 #normWeightMode="trace+cv"
-normWeightMode="trace"
+#normWeightMode="trace"
 #print(normWeightMode)
 #In future, you may need to comment line 44 to use this functionality if you do
 #weighting not just in normalization.

gemme.py

@@ -255,9 +255,14 @@ def parse_command_line():
         help='fasta file containing related sequences',
         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('--normweightmode', dest='normweightmode', type=str, \
+        help="It can be one of these: 'trace', 'trace+pc', 'trace+cv' or 'trace+pc+cv'. Default is 'trace'.",
+        required=False, default="trace")
 
     args = parser.parse_args()
 
@@ -267,14 +272,15 @@ def parse_command_line():
  
     # Check flag arguments
     if args.input is None:
-    	parser.error("gemme requires an input alignment.")
+    	parser.error("GEMME requires an input alignment.")
 
     return args
 
 
-def doit(inAli,mutFile,retMet,bFile,fFile,n,N, isjet2on):
+def doit(inAli,mutFile,retMet,bFile,fFile,n,N, isjet2on, normWeightMode):
     """
-    Fonksiyon aciklamasi ile taniminin ayni olmasi super olmus!
+    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)
     """
     simple = True
@@ -298,7 +304,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, isjet2on):
     else:
         print("ERROR: You can only use true or false after --isjet2on!")
         sys.exit(-1)
-    launchPred(prot,inAli,mutFile)
+    launchPred(prot,inAli,mutFile, normWeightMode)
 
     #Do Python plotting here
     #TODO: Eventually, I will do the map plotting with a completely independent 
@@ -344,7 +350,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, isjet2on):
 def main():
     args = parse_command_line()
     doit(args.input,args.mutations,args.retrievingMethod,args.blastFile,\
-         args.fastaFile,args.nIter,args.NSeqs, args.isjet2on)
+         args.fastaFile,args.nIter,args.NSeqs, args.isjet2on, args.normweightmode)
 
 if (__name__ == '__main__'):
     main()

gemmeAnal.py

@@ -135,12 +135,12 @@ def launchJET(prot,retMet,bFile,fFile,n,N,nl):
 	return(reCode)
 
 # Run Rscript to compute predictions
-def launchPred(prot,inAli,mutFile):
+def launchPred(prot,inAli,mutFile, normWeightMode):
 
 	if mutFile!='':
-		rcmd="Rscript --save $GEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile
+		rcmd="Rscript --save $GEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode
 	else:
-		rcmd="Rscript --save $GEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none"
+		rcmd="Rscript --save $GEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode
 
 	print("\nRunning: \n"+rcmd)
 	reCode=subprocess.call(rcmd,shell=True)