Commit e6123f25 by Mustafa Tekpinar

Removed unused coilbreakerlength argument.

parent e86e4bf6
...@@ -791,7 +791,8 @@ def check_argument_groups(parser, arg_dict, group, argument): ...@@ -791,7 +791,8 @@ def check_argument_groups(parser, arg_dict, group, argument):
parser.error("escott requires " + group + parser.error("escott requires " + group +
" to be set to input if " + str(argument) + " is used.") " to be set to input if " + str(argument) + " is used.")
return None return None
def calculateSecondaryStructure(pdbfile, coilBreakerLength): # def calculateSecondaryStructure(pdbfile, coilBreakerLength):
def calculateSecondaryStructure(pdbfile):
""" """
Calls dssp, calculates secondary structure and saves the results as a Calls dssp, calculates secondary structure and saves the results as a
text file with .dssp extention. The result contains a residue index and text file with .dssp extention. The result contains a residue index and
...@@ -993,9 +994,9 @@ def parse_command_line(): ...@@ -993,9 +994,9 @@ def parse_command_line():
help="If coil length is > maxcoillength, it will use JET values.", help="If coil length is > maxcoillength, it will use JET values.",
required=False, default=5) required=False, default=5)
parser.add_argument('--coilbreakerlength', dest='coilbreakerlength', type=int, \ # parser.add_argument('--coilbreakerlength', dest='coilbreakerlength', type=int, \
help="Length of coil breaking S or T residues between C(S|T)C pattern.", # help="Length of coil breaking S or T residues between C(S|T)C pattern.",
required=False, default=1) # required=False, default=1)
args = parser.parse_args() args = parser.parse_args()
...@@ -1011,7 +1012,7 @@ def parse_command_line(): ...@@ -1011,7 +1012,7 @@ def parse_command_line():
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, verbosity, offset, colormap, maxCoilLength = 5, coilbreakerlength=1): alphabet, verbosity, offset, colormap, maxCoilLength = 5):
""" """
Perfect explanation for a function: typing the function call exactly! Perfect explanation for a function: typing the function call exactly!
doit is basically the main function in disguise! doit is basically the main function in disguise!
...@@ -1082,7 +1083,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode, ...@@ -1082,7 +1083,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
print("ERROR: There is not any pdb file.") print("ERROR: There is not any pdb file.")
sys.exit(-1) sys.exit(-1)
else: else:
calculateSecondaryStructure(pdbfile, coilbreakerlength) calculateSecondaryStructure(pdbfile)
countCoilSegments(pdbfile+".dssp") countCoilSegments(pdbfile+".dssp")
df = pd.read_table(prot+"_jet.res", sep="\s+") 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, ...@@ -1119,7 +1120,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
print("ERROR: There is not any pdb file.") print("ERROR: There is not any pdb file.")
sys.exit(-1) sys.exit(-1)
else: else:
calculateSecondaryStructure(pdbfile, coilbreakerlength) calculateSecondaryStructure(pdbfile)
countCoilSegments(pdbfile+".dssp") countCoilSegments(pdbfile+".dssp")
df = pd.read_table(prot+"_jet.res", sep="\s+") 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, ...@@ -1156,7 +1157,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
print("ERROR: There is not any pdb file.") print("ERROR: There is not any pdb file.")
sys.exit(-1) sys.exit(-1)
else: else:
calculateSecondaryStructure(pdbfile, coilbreakerlength) calculateSecondaryStructure(pdbfile)
countCoilSegments(pdbfile+".dssp") countCoilSegments(pdbfile+".dssp")
df = pd.read_table(prot+"_jet.res", sep="\s+") 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, ...@@ -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()} threeLetters2oneLetter = {v: k for k, v in oneLetter2ThreeLetters.items()}
calculateSecondaryStructure(pdbfile, coilbreakerlength) calculateSecondaryStructure(pdbfile)
countCoilSegments(pdbfile+".dssp") countCoilSegments(pdbfile+".dssp")
df = pd.read_table(prot+"_jet.res", sep="\s+") df = pd.read_table(prot+"_jet.res", sep="\s+")
...@@ -1451,8 +1452,7 @@ def main(): ...@@ -1451,8 +1452,7 @@ def main():
doit(args.input, args.mutations, args.retrievingMethod, args.blastFile,\ doit(args.input, args.mutations, args.retrievingMethod, args.blastFile,\
args.fastaFile, args.nIter,args.NSeqs, args.jetfile, args.pdbfile,\ args.fastaFile, args.nIter,args.NSeqs, args.jetfile, args.pdbfile,\
args.normweightmode, args.alphabet, args.verbose, args.offset, \ args.normweightmode, args.alphabet, args.verbose, args.offset, \
args.colormap, maxCoilLength=args.maxcoillength, \ args.colormap, maxCoilLength=args.maxcoillength)
coilbreakerlength=args.coilbreakerlength)
toc = time.perf_counter() toc = time.perf_counter()
......
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