alphabet selection was added as an input argument!

computePred.R

@@ -23,6 +23,7 @@ aliFile = args[2]
 simple = args[3]
 fname = args[4]
 normWeightMode = args[5]
+selectedAlphabet = args[6]
 
 # read alignment and convert to matrix
 ali=as.matrix.alignment(read.alignment(aliFile,format="fasta"))
@@ -241,7 +242,8 @@ print(alpha)
 
 
 
-alphabet = "lz-bl.7"
+#alphabet = "lz-bl.7"
+alphabet = selectedAlphabet
 if(simple){
   normPredCombi = normalizePredWithNbSeqsPC(pred,trace,wt,alpha,nbSeqs,alphabet)
   rownames(normPredCombi)=aa

gemme.py

@@ -363,6 +363,10 @@ def parse_command_line():
         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('--alphabet', dest='alphabet', type=str, \
+        help="Which alphabet to use. Default is lz-bl.7",
+        required=False, default="lz-bl.7")
+
     retMet_args.add_argument('-p', '--pdbfile', dest='pdbfile', type=str, \
         help="If a pdb file is provided, it will skip fake pdb file production step and use that file. Default is None",
         required=False, default=None)
@@ -384,7 +388,7 @@ def parse_command_line():
     return args
 
 
-def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode):
+def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode, alphabet):
     """
     Perfect explanation for a function: typing the function call exactly!
     doit is basically the main function in disguise!
@@ -468,7 +472,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
 
         print(df)
 
-    launchPred(prot,inAli,mutFile, normWeightMode)
+    launchPred(prot,inAli,mutFile, normWeightMode, alphabet)
 
     #Do Python plotting here
     #TODO: Eventually, I will do the map plotting with a completely independent 
@@ -514,7 +518,8 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
 def main():
     args = parse_command_line()
     doit(args.input,args.mutations,args.retrievingMethod,args.blastFile,\
-         args.fastaFile,args.nIter,args.NSeqs, args.jetfile, args.pdbfile, args.normweightmode)
+         args.fastaFile,args.nIter,args.NSeqs, args.jetfile, args.pdbfile,\
+         args.normweightmode, args.alphabet)
 
 if (__name__ == '__main__'):
     main()

gemmeAnal.py

@@ -172,12 +172,12 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 	return(reCode)
 
 # Run Rscript to compute predictions
-def launchPred(prot,inAli,mutFile, normWeightMode):
+def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
 
 	if mutFile!='':
-		rcmd="Rscript --save $GEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode
+		rcmd="Rscript --save $GEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
 	else:
-		rcmd="Rscript --save $GEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode
+		rcmd="Rscript --save $GEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
 
 	print("\nRunning: \n"+rcmd)
 	reCode=subprocess.call(rcmd,shell=True)