Added --maxcoillength argument.

esgemme/esgemme.py

@@ -267,7 +267,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
                         prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" -a 3"+" > "+prot+".out"
                         #One can also add: -g 'trace,pc,cv,clusters,axs' 
                 
-                print("\nRunning for SC1:\n"+jetcmd)
+                print("\nRunning JET2 with following arguments:\n"+jetcmd)
                 reCode=subprocess.call(jetcmd,shell=True)
                 if os.path.isfile(prot+"/"+prot+"_jet.res"):
                     os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
@@ -334,7 +334,7 @@ def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
         # rcmd="Rscript --save $ESGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
         rcmd="Rscript --save computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
 
-    print("\nRunning: \n"+rcmd)
+    print("\nRunning Rscript with following arguments: \n"+rcmd)
     reCode=subprocess.call(rcmd,shell=True)
 
 	#Add plots here with gemmemore
@@ -955,6 +955,10 @@ def parse_command_line():
         help="Select a colormap from standard matplotlib colormaps",
         required=False, default='Oranges_r')
     
+    parser.add_argument('--maxcoillength', dest='maxcoillength', type=int, \
+        help="If coil length is > maxcoillength, it will use JET values.",
+        required=False, default=5)
+    
     args = parser.parse_args()
 
     arg_dict = vars(args)
@@ -969,12 +973,13 @@ def parse_command_line():
 
 
 def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,\
-         alphabet, verbosity, offset, colormap):
+         alphabet, verbosity, offset, colormap, maxCoilLength = 5):
     """
     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.jetfile)
     """
+    debug = 0
     if(mutFile != ''):
         simple = False
     else:
@@ -1040,18 +1045,21 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             countCoilSegments(pdbfile+".dssp")
 
             df = pd.read_table(prot+"_jet.res", sep="\s+")
-            print(df['pos'])
-            print(pdbfile+".dssp")
-            print(os.getcwd())
-            df2 = pd.read_table(pdbfile+".dssp.new", header=None, sep=",")
 
+            df2 = pd.read_table(pdbfile+".dssp.new", header=None, sep=",")
             df2.columns = ['pos', 'ss', 'length']
-            print(df2)
 
             mergedRes = pd.merge(df, df2, on ='pos', right_index=False)
+
+            if(debug):
+                print(df['pos'])
+                print(pdbfile+".dssp")
+                print(os.getcwd())
+                print(df2)            
                 print(mergedRes)
+
             sstjetormaxList = []
-            maxCoilLength = 5
+            # maxCoilLength = 5
             print("WARNING: Max. coil length = {}".format(maxCoilLength))
             for index, row in mergedRes.iterrows():
                 if(row['ss']=='C') and (row['length']>maxCoilLength):
@@ -1245,7 +1253,8 @@ 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)
+         args.normweightmode, args.alphabet, args.verbose, args.offset, \
+         args.colormap, maxCoilLength=args.maxcoillength)
 
     toc = time.perf_counter()