Removed unused coilbreakerlength argument.

prescott/escott.py

@@ -791,7 +791,8 @@ def check_argument_groups(parser, arg_dict, group, argument):
             parser.error("escott requires " + group +
                          " to be set to input if " + str(argument) + " is used.")
     return None
-def calculateSecondaryStructure(pdbfile, coilBreakerLength):
+# def calculateSecondaryStructure(pdbfile, coilBreakerLength):
+def calculateSecondaryStructure(pdbfile):
     """
         Calls dssp, calculates secondary structure and saves the results as a 
         text file with .dssp extention. The result contains a residue index and 
@@ -993,9 +994,9 @@ def parse_command_line():
         help="If coil length is > maxcoillength, it will use JET values.",
         required=False, default=5)
     
-    parser.add_argument('--coilbreakerlength', dest='coilbreakerlength', type=int, \
-        help="Length of coil breaking S or T residues between C(S|T)C pattern.",
-        required=False, default=1)
+    # parser.add_argument('--coilbreakerlength', dest='coilbreakerlength', type=int, \
+    #     help="Length of coil breaking S or T residues between C(S|T)C pattern.",
+    #     required=False, default=1)
     
     args = parser.parse_args()
 
@@ -1011,7 +1012,7 @@ def parse_command_line():
 
 
 def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,\
-         alphabet, verbosity, offset, colormap, maxCoilLength = 5, coilbreakerlength=1):
+         alphabet, verbosity, offset, colormap, maxCoilLength = 5):
     """
     Perfect explanation for a function: typing the function call exactly!
     doit is basically the main function in disguise!
@@ -1082,7 +1083,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             print("ERROR: There is not any pdb file.")
             sys.exit(-1)
         else:
-            calculateSecondaryStructure(pdbfile, coilbreakerlength)
+            calculateSecondaryStructure(pdbfile)
             countCoilSegments(pdbfile+".dssp")
 
             df = pd.read_table(prot+"_jet.res", sep="\s+")
@@ -1119,7 +1120,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             print("ERROR: There is not any pdb file.")
             sys.exit(-1)
         else:
-            calculateSecondaryStructure(pdbfile, coilbreakerlength)
+            calculateSecondaryStructure(pdbfile)
             countCoilSegments(pdbfile+".dssp")
 
             df = pd.read_table(prot+"_jet.res", sep="\s+")
@@ -1156,7 +1157,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             print("ERROR: There is not any pdb file.")
             sys.exit(-1)
         else:
-            calculateSecondaryStructure(pdbfile, coilbreakerlength)
+            calculateSecondaryStructure(pdbfile)
             countCoilSegments(pdbfile+".dssp")
 
             df = pd.read_table(prot+"_jet.res", sep="\s+")
@@ -1220,7 +1221,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
 
             threeLetters2oneLetter = {v: k for k, v in oneLetter2ThreeLetters.items()}
 
-            calculateSecondaryStructure(pdbfile, coilbreakerlength)
+            calculateSecondaryStructure(pdbfile)
             countCoilSegments(pdbfile+".dssp")
 
             df = pd.read_table(prot+"_jet.res", sep="\s+")
@@ -1451,8 +1452,7 @@ def main():
     doit(args.input, args.mutations, args.retrievingMethod, args.blastFile,\
          args.fastaFile, args.nIter,args.NSeqs, args.jetfile, args.pdbfile,\
          args.normweightmode, args.alphabet, args.verbose, args.offset, \
-         args.colormap, maxCoilLength=args.maxcoillength, \
-        coilbreakerlength=args.coilbreakerlength)
+         args.colormap, maxCoilLength=args.maxcoillength)
 
     toc = time.perf_counter()