Changed normWeightMode options.

Convert trace->tjet, maxhalftracepchalftracecvhalfcvpc->max
and ssjetormax->sstjetormax in ESGEMME.

computePred.R

@@ -46,7 +46,7 @@ res = list(computePSSM(ali,N[1],npos),computePSSM(aliCons,N[2],npos),computePSSM
 jet=read.table(paste(prot,"_jet.res",sep=""),head=TRUE)
 ############################################Added by MT to test effect of PC, CV, DFI, Bfactor etc.
 trace = c()
-if ((normWeightMode=="maxhalftracepchalftracecvhalfcvpc")){
+if ((normWeightMode=="max")){
   print(paste("Using ", normWeightMode))
   for (row in 1:nrow(jet)) {
     if(sum(colnames(jet)=="traceMax")==1){
@@ -55,8 +55,8 @@ if ((normWeightMode=="maxhalftracepchalftracecvhalfcvpc")){
       trace<-append(trace, max((jet[row, "trace"]+jet[row, "pc"])/2.0, max((jet[row, "trace"]+jet[row, "cv"])/2.0, (jet[row, "pc"]+jet[row, "cv"])/2.0 )))
     }
   }
-}else if (normWeightMode=="trace"){
-  print("Using only JET2 traces")
+}else if (normWeightMode=="tjet"){
+  print("Using only T_JET2 traces")
   for (row in 1:nrow(jet)) {
     if(sum(colnames(jet)=="traceMax")==1){
       trace<-append(trace, jet[row, "traceMax"])
@@ -74,22 +74,21 @@ if ((normWeightMode=="maxhalftracepchalftracecvhalfcvpc")){
   for (row in 1:nrow(jet)) {
     trace<-append(trace, jet[row, "pc"]) 
   }
-}else if (normWeightMode=="ssjetormax"){
-  print("Using only ssjetormax")
+}else if (normWeightMode=="sstjetormax"){
+  print("Using only sstjetormax")
   for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="ssjetormax")==1){
-      trace<-append(trace, jet[row, "ssjetormax"])
+    if(sum(colnames(jet)=="sstjetormax")==1){
+      trace<-append(trace, jet[row, "sstjetormax"])
     }else{
-      print("No field called ssjetormax in the JET output!")
+      print("No field called sstjetormax in the JET output!")
       quit(status=-1)
     } 
   }
 
 }else{
   print("ERROR: Unknown --normWeightMode selected!")
-  print("It can only be 'trace', 'pc', 'cv',")
-  print("'maxhalftracepchalftracecvhalfcvpc'")
-  print(" or 'ssjetormax'!")
+  print("It can only be 'tjet', 'pc', 'cv',")
+  print("'max' or 'sstjetormax'!")
 }
 print(trace)
 #####################################################################################################################

esgemme.py

@@ -296,8 +296,8 @@ def cleanTheMess(prot,bFile,fFile, chainID):
         if fFile!=prot+"_"+chainID+".fasta":
             if os.path.isfile(prot+"_"+chainID+".fasta"):
                 os.remove(prot+"_"+chainID+".fasta")		
-    if os.path.isfile(prot+"_jet.res"):
-        os.remove(prot+"_jet.res")
+    # if os.path.isfile(prot+"_jet.res"):
+    #     os.remove(prot+"_jet.res")
     if os.path.isfile(prot+".pdb"):
         os.remove(prot+".pdb")
 	
@@ -820,10 +820,9 @@ def parse_command_line():
         required=False, default=None)
     
     retMet_args.add_argument('--normweightmode', dest='normweightmode', type=str, \
-        help="It can be one of these: 'trace', 'tracemovingaverage', 'cv', 'pc', 'dfi', 'maxtracesc',"+\
-            "'maxtracepc', 'maxtracecv', 'maxtracepccv', 'maxtracepcsc', 'maxtracepchalfpccv', "+\
-            "'halfcvpc', maxhalftracepchalftracecvhalfcvpc or jetormax. Default is 'trace'.",
-        required=False, default="trace")
+        help="It can be one of these: 'tjet', 'cv', 'pc',"+\
+            "max or sstjetormax. Default is 'tjet'.",
+        required=False, default="tjet")
 
     args = parser.parse_args()
 
@@ -863,13 +862,13 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
 
     print("query protein: "+prot)
     
-    if( (normWeightMode != 'trace') and \
+    if( (normWeightMode != 'tjet') and \
         (normWeightMode != 'cv') and \
         (normWeightMode != 'pc') and \
-        (normWeightMode != 'maxhalftracepchalftracecvhalfcvpc') and \
-        (normWeightMode != 'ssjetormax')):
-        print("ERROR: normWeightMode can only be 'trace', 'cv', 'pc', "+\
-              "'maxhalftracepchalftracecvhalfcvpc' or 'ssjetormax'!")
+        (normWeightMode != 'max') and \
+        (normWeightMode != 'sstjetormax')):
+        print("ERROR: normWeightMode can only be 'tjet', 'cv', 'pc', "+\
+              "'max' or 'sstjetormax'!")
         sys.exit(-1)
 
     structure = parsePDB(prot+".pdb")
@@ -899,31 +898,14 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             shutil.copy2(jetfile, prot+"_jet.res")
         print("done")
 
-    # #If a real pdb file is given, calculate dfi for the residues. 
-    # if(((normWeightMode=='dfi') or (normWeightMode=='maxtracedfi') or (normWeightMode=='maxdfitrace'))):
-    #     if (pdbfile == None):
-    #         print("ERROR: There is not any pdb file to calculate DFI.")
-    #         sys.exit(-1)
-    #     else:
-    #         print("Calculating %DFI data per residue!")
-    #         dfi = calcPercentDFI(pdbfile, outfile=None, nmodes=None, attenuate="true", ranksorted="true")
-    #         dfi = dfi
-    #         df = pd.read_table(prot+"_jet.res")
-    #         print(df)
-
-    #         df['dfi'] = dfi.round(4)
-    #         df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
-
-    #         print(df)
-    if((normWeightMode=='ssjetormax')):
+    if((normWeightMode=='sstjetormax')):
         if (pdbfile == None):
-            print("ERROR: There is not any pdb file to calculate DFI.")
+            print("ERROR: There is not any pdb file.")
             sys.exit(-1)
         else:
             calculateSecondaryStructure(pdbfile)
             countCoilSegments(pdbfile+".dssp")
-            #os.system("python /home/tekpinar/software/scripts/python_scripts/biotite-secondary-structure.py "+pdbfile+" "+pdbfile+".dssp")
-            #os.system("python /home/tekpinar/software/scripts/python_scripts/count-coil-segments-v2.py "+pdbfile+".dssp >"+pdbfile+".dssp.new")
+
             df = pd.read_table(prot+"_jet.res", sep="\s+")
             print(df['pos'])
             print(pdbfile+".dssp")
@@ -935,46 +917,46 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
             
             mergedRes = pd.merge(df, df2, on ='pos', right_index=False)
             print(mergedRes)
-            ssjetormaxList = []
+            sstjetormaxList = []
             maxCoilLength = 5
             print("WARNING: Max. coil length = {}".format(maxCoilLength))
             for index, row in mergedRes.iterrows():
                 if(row['ss']=='C') and (row['length']>maxCoilLength):
-                    ssjetormaxList.append(row['trace'])
+                    sstjetormaxList.append(row['trace'])
                 else:
                     maxVal = max([((row['trace']+row['pc'])/2.0), ((row['trace']+row['cv'])/2.0), ((row['cv']+row['pc'])/2.0)])
-                    ssjetormaxList.append(maxVal)
-            #ssjetormaxList=rankSortProteinData(ssjetormaxList, inverted=False)
-            df['ssjetormax'] = ssjetormaxList
-            df['ssjetormax'] = df['ssjetormax'].round(decimals = 4)
+                    sstjetormaxList.append(maxVal)
+            #sstjetormaxList=rankSortProteinData(sstjetormaxList, inverted=False)
+            df['sstjetormax'] = sstjetormaxList
+            df['sstjetormax'] = df['sstjetormax'].round(decimals = 4)
             df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
             #sys.exit(-1)
 
-    #If a real pdb file is given, calculate dfi for the residues. 
-    if(((normWeightMode=='tracemovingaverage'))):
-        print("Calculating trace moving average per residue!")
-        # tma = tracemovingaverage
-        df = pd.read_csv(prot+"_jet.res", delimiter=r"\s+") 
-        print(df.columns)
-        # Get the window of series
-        # of observations of specified window size
-        window_size = 3
-        windows = df['trace'].rolling(window_size)
+    # #If a real pdb file is given, calculate dfi for the residues. 
+    # if(((normWeightMode=='tracemovingaverage'))):
+    #     print("Calculating trace moving average per residue!")
+    #     # tma = tracemovingaverage
+    #     df = pd.read_csv(prot+"_jet.res", delimiter=r"\s+") 
+    #     print(df.columns)
+    #     # Get the window of series
+    #     # of observations of specified window size
+    #     window_size = 3
+    #     windows = df['trace'].rolling(window_size)
         
-        # Create a series of moving
-        # averages of each window
-        moving_averages = windows.mean()
-        tma = moving_averages
+    #     # Create a series of moving
+    #     # averages of each window
+    #     moving_averages = windows.mean()
+    #     tma = moving_averages
 
-        print(df)
+    #     print(df)
 
-        df['tracemovingaverage'] = tma.round(4)
-        #The first two elements are just copied bc they don't exist due to the moving average. 
-        df['tracemovingaverage'].iloc[0] = df['trace'].iloc[0].round(4)
-        df['tracemovingaverage'].iloc[1] = df['trace'].iloc[1].round(4)
-        df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
+    #     df['tracemovingaverage'] = tma.round(4)
+    #     #The first two elements are just copied bc they don't exist due to the moving average. 
+    #     df['tracemovingaverage'].iloc[0] = df['trace'].iloc[0].round(4)
+    #     df['tracemovingaverage'].iloc[1] = df['trace'].iloc[1].round(4)
+    #     df.to_csv(prot+"_jet.res", header=True, index=None, sep='\t', mode='w')
 
-        print(df)
+    #     print(df)
     # #If a real pdb file is given, calculate or get Bfactors for the residues. 
     # if(((normWeightMode=='bfactor') or (normWeightMode=='maxtracebfactor') or (normWeightMode=='maxbfactortrace'))):
     #     isCalc = True

examples/example-esgemme-script.sh

@@ -27,7 +27,7 @@ then
     echo "Using blat-af2.pdb for the structural feature calculations!"
     echo "Entire mutational map of the protein will be calculated!"
     python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
-	   --pdbfile ../data/blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc
+	   --pdbfile ../data/blat-af2.pdb --normweightmode max
 
 elif [ "$1" == "withpdb-withmutfile" ]
 then
@@ -36,17 +36,17 @@ then
     echo "Using blat-af2.pdb for the structural feature calculations!"
     echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
     python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta  \
-	   --pdbfile ../data/blat-af2.pdb --normweightmode maxhalftracepchalftracecvhalfcvpc \
+	   --pdbfile ../data/blat-af2.pdb --normweightmode max \
 	   -m ../data/Stiffler_2015_BLAT_ECOLX.mut
 
-elif [ "$1" == "ssjetormax" ]
+elif [ "$1" == "sstjetormax" ]
 then
 
     #Please note that CV isa structural feature and it can not be calculated if you don't specify a pdb file.
     echo "Using blat-af2.pdb for the secondary structure based calculations!"
     echo "Only effects of mutations specified in the Stiffler_2015_BLAT_ECOLX.mut file will be calculated!"
     python $ESGEMME_PATH/esgemme.py ../data/aliBLAT.fasta -r input -f ../data/aliBLAT.fasta \
-	   --pdbfile ../data/blat-af2.pdb --normweightmode ssjetormax \
+	   --pdbfile ../data/blat-af2.pdb --normweightmode sstjetormax \
 	   -m ../data/Stiffler_2015_BLAT_ECOLX.mut
     
 else