Added --verbose option to the esgemme.py arguments.

--verbose option controls if epistatic and independent
results files will be written or not. It is False by
default and therefore, the files are not written.

esgemme.py

@@ -317,7 +317,7 @@ def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
     return(reCode)
 
 # Remove temporary files
-def cleanTheMess(prot,bFile,fFile, chainID):
+def cleanTheMess(prot,bFile,fFile, chainID, verbosity=False):
 
     if bFile!='':
         if bFile!=prot+"_"+chainID+".psiblast":
@@ -360,6 +360,13 @@ def cleanTheMess(prot,bFile,fFile, chainID):
 
     if os.path.isfile("default.conf"):
         os.remove("default.conf")
+
+    if verbosity == False:
+        if os.path.isfile(prot+"_normPred_evolInd.txt"):
+            os.remove(prot+"_normPred_evolInd.txt")
+        if os.path.isfile(prot+"_normPred_evolEpi.txt"):
+            os.remove(prot+"_normPred_evolEpi.txt")
+       
     
 ###############################################################################
 def rankSortProteinData(dataArray, inverted=True):
@@ -777,7 +784,7 @@ def countCoilSegments(inputfile):
 def parse_command_line():
     """
         Parse command line.
-        It uses argparse to parse esgemme' command line arguments and returns the
+        It uses argparse to parse 'esgemme' command line arguments and returns the
         argparse parser.
     """
     parser = argparse.ArgumentParser(
@@ -802,7 +809,10 @@ def parse_command_line():
 
     parser.add_argument(
         '-m', '--mutations',
-        help='text file containing the mutations of interest. Each line of the file should contain a mutation (e.g. D136R) or combination of mutations separated by commas and ordered according to their positions in the sequence (e.g. D136R,V271A)',
+        help='text file containing the mutations of interest. Each line of the '+\
+             'file should contain a mutation (e.g. D136R) or combination of '+\
+             'mutations separated by colons and ordered according to their '+\
+             'positions in the sequence (e.g. D136R:V271A)',
         default=''
     )
 
@@ -844,19 +854,25 @@ 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, \
+    parser.add_argument('--alphabet', dest='alphabet', type=str, \
         help="Which alphabet to use. Default is lw-i.7",
         required=False, default="lw-i.7")
 
-    retMet_args.add_argument('-p', '--pdbfile', dest='pdbfile', type=str, \
+    parser.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)
     
-    retMet_args.add_argument('--normweightmode', dest='normweightmode', type=str, \
+    parser.add_argument('--normweightmode', dest='normweightmode', type=str, \
         help="It can be one of these: 'tjet', 'cv', 'pc',"+\
             "max, tjetormax or sstjetormax. Default is 'tjet'.",
         required=False, default="tjet")
 
+    parser.add_argument('--verbose', dest='verbose', type=bool, \
+        help="This argument controls amount of the output. Default is 'False'."+\
+             "If it is set to 'True', it will print independent and epistatic"+\
+             "score files as well combined combined score file.",
+        required=False, default=False)
+    
     args = parser.parse_args()
 
     arg_dict = vars(args)
@@ -870,7 +886,7 @@ def parse_command_line():
     return args
 
 
-def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode, alphabet):
+def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode, alphabet, verbosity):
     """
     Perfect explanation for a function: typing the function call exactly!
     doit is basically the main function in disguise!
@@ -1032,22 +1048,16 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
     if(simple):
         print("generating the plots...")
         #Check if the normalized data files were created. 
-        if(os.path.exists(prot+"_normPred_evolEpi.txt")):
+        if(os.path.exists(prot+"_normPred_evolEpi.txt") and args.verbose==True):
             gemmeData = parseGEMMEoutput(prot+"_normPred_evolEpi.txt", verbose=False)
             plotGEMMEmatrix(gemmeData, prot+"_normPred_evolEpi.png", 1, None,\
                             colorMap='Blues_r', offSet=0, pixelType='square')
-        else:
-            print("ERROR: "+prot+"_normPred_evolEpi.txt file does not exist!")
-            print("       Can not generate "+prot+"_normPred_evolEpi.png file!")
         
         #Check if the normalized data files were created. 
-        if(os.path.exists(prot+"_normPred_evolInd.txt")):
+        if(os.path.exists(prot+"_normPred_evolInd.txt") and args.verbose==True):
             gemmeData = parseGEMMEoutput(prot+"_normPred_evolInd.txt", verbose=False)
             plotGEMMEmatrix(gemmeData, prot+"_normPred_evolInd.png", 1, None,\
                             colorMap='Greens_r', offSet=0, pixelType='square')
-        else:
-            print("ERROR: "+prot+"_normPred_evolInd.txt file does not exist!")
-            print("       Can not generate "+prot+"_normPred_evolInd.png file!")
 
         #Check if the normalized data files were created. 
         if(os.path.exists(prot+"_normPred_evolCombi.txt")):        
@@ -1073,14 +1083,13 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             #print(df['pos'])
             gemmeDFtrans.to_csv(prot+"_normPred_evolCombiTransposed.txt", sep='\t', float_format='%.2f', na_rep='NaN')
             #sys.exit(-1)
-            
-            
+
         else:
             print("ERROR: "+prot+"_normPred_evolCombi.txt file does not exist!")
             print("       Can not generate "+prot+"_normPred_evolCombi.png file!")
         print("done")
 
-    cleanTheMess(prot,bFile,fFile, chainID=chains[0])
+    cleanTheMess(prot,bFile,fFile, chainID=chains[0], verbosity=verbosity)
 
 if (__name__ == '__main__'):
     tic = time.perf_counter()
@@ -1088,7 +1097,7 @@ if (__name__ == '__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.alphabet)
+         args.normweightmode, args.alphabet, args.verbose)
 
     toc = time.perf_counter()