Added more options to the normweightmode!

computePred.R

@@ -127,16 +127,26 @@ if((normWeightMode=="max-trace-pc") | (normWeightMode=="max-pc-trace")){
       trace<-append(trace, max(jet[row, "trace"], max(jet[row, "pc"], jet[row, "cv"])))
     }
   }
-} else if ((normWeightMode=="half-cv+pc") | (normWeightMode=="half-pc+cv")){
+} else if ((normWeightMode=="max-trace-half-pc+cv")|(normWeightMode=="max-trace-half-cv+pc")){
   print(paste("Using ", normWeightMode))
   for (row in 1:nrow(jet)) {
     if(sum(colnames(jet)=="traceMax")==1){
-      trace<-append(trace, max(jet[row, "traceMax"], jet[row, "cv"]))
+      trace<-append(trace, max(jet[row, "traceMax"], (jet[row, "pc"]+jet[row, "cv"])/2.0 ))
     }else{
+      trace<-append(trace, max(jet[row, "trace"], (jet[row, "pc"]+jet[row, "cv"])/2.0 ))
+    }
+  }
+}else if ((normWeightMode=="half-cv+pc") | (normWeightMode=="half-pc+cv")){
+  print(paste("Using ", normWeightMode))
+  for (row in 1:nrow(jet)) {
     trace<-append(trace, (jet[row, "pc"]+jet[row, "cv"])/2.0)
     }  
+} else if ((normWeightMode=="max-cv-pc") | (normWeightMode=="max-pc-cv")){
+  print(paste("Using ", normWeightMode))
+  for (row in 1:nrow(jet)) {
+    trace<-append(trace, max(jet[row, "pc"], jet[row, "cv"]))
     }  
-} else if (normWeightMode=="trace"){
+}else if (normWeightMode=="trace"){
   print("Using only JET2 traces")
   for (row in 1:nrow(jet)) {
     if(sum(colnames(jet)=="traceMax")==1){
@@ -145,9 +155,19 @@ if((normWeightMode=="max-trace-pc") | (normWeightMode=="max-pc-trace")){
       trace<-append(trace, jet[row, "trace"])
     } 
   }
+}else if (normWeightMode=="cv"){
+  print("Using only CV traces")
+  for (row in 1:nrow(jet)) {
+    trace<-append(trace, jet[row, "cv"]) 
+  }
+}else if (normWeightMode=="pc"){
+  print("Using only PC traces")
+  for (row in 1:nrow(jet)) {
+    trace<-append(trace, jet[row, "pc"]) 
+  }
 }else{
   print("ERROR: Unknown --normWeightMode selected!")
-  print("It can only be 'trace', 'max-trace-pc', 'max-trace-cv', 'max-trace-pc-cv' or 'half-cv+pc'!")
+  print("It can only be 'trace', 'pc', 'cv', 'max-trace-pc', 'max-trace-cv', 'max-trace-pc-cv' or 'half-cv+pc'!")
 }
 print(trace)
 

gemme.py

@@ -304,15 +304,21 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode)
     print("query protein: "+prot)
     
     if( (normWeightMode != 'trace') and \
+        (normWeightMode != 'cv') and \
+        (normWeightMode != 'pc') and \
         (normWeightMode != 'max-trace-pc') and \
         (normWeightMode != 'max-pc-trace') and \
+        (normWeightMode != 'max-pc-cv') and \
+        (normWeightMode != 'max-cv-pc') and \
         (normWeightMode != 'max-trace-cv') and \
         (normWeightMode != 'max-cv-trace') and \
         (normWeightMode != 'max-trace-pc-cv') and \
         (normWeightMode != 'max-trace-cv-pc') and \
         (normWeightMode != 'half-pc+cv') and \
-        (normWeightMode != 'half-cv+pc')):
-        print("ERROR: normWeightMode can only be 'trace', 'max-trace-pc', 'max-trace-cv', 'max-trace-pc-cv' or 'half-cv+pc'!")
+        (normWeightMode != 'half-cv+pc') and \
+        (normWeightMode != 'max-trace-half-cv+pc') and \
+        (normWeightMode != 'max-trace-half-pc+cv')):
+        print("ERROR: normWeightMode can only be 'trace', 'cv', 'pc', 'max-trace-pc', 'max-pc-cv', 'max-trace-cv', 'max-trace-pc-cv', 'half-cv+pc' or max-trace-half-cv+pc!")
         sys.exit(-1)
 
     if((jetfile) == None):