Removed unused normWeightMode options in esgemme.py and computePred.R.

computePred.R

@@ -46,88 +46,7 @@ write.table(res[[3]][[3]],paste0(prot,"_pssm80.txt"))
 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=="maxtracepc") | (normWeightMode=="maxpctrace")){
-  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, "pc"]))
-    }else{
-        trace<-append(trace, max(jet[row, "trace"], jet[row, "pc"]))
-    }
-  }
-} else if ((normWeightMode=="maxtracecv") | (normWeightMode=="maxcvtrace")){
-  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"]))
-    }else{
-        trace<-append(trace, max(jet[row, "trace"], jet[row, "cv"]))
-    } 
-  }
-} else if ((normWeightMode=="maxtracesc") | (normWeightMode=="maxsctrace")){
-  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, "clusters"]))
-    }else{
-        trace<-append(trace, max(jet[row, "trace"], jet[row, "clusters"]))
-    } 
-  }
-} else if ((normWeightMode=="maxtracedfi") | (normWeightMode=="maxdfitrace")){
-  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, "dfi"]))
-    }else{
-        trace<-append(trace, max(jet[row, "trace"], jet[row, "dfi"]))
-    } 
-  }
-} else if ((normWeightMode=="maxtracebfactor") | (normWeightMode=="maxbfactortrace")){
-  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, "bfactor"]))
-    }else{
-        trace<-append(trace, max(jet[row, "trace"], jet[row, "bfactor"]))
-    } 
-  }
-}else if ((normWeightMode=="maxtracepccv")|(normWeightMode=="maxtracecvpc")){
-  print(paste("Using ", normWeightMode))
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="traceMax")==1){
-      trace<-append(trace, max(jet[row, "traceMax"], max(jet[row, "pc"], jet[row, "cv"])))
-    }else{
-      trace<-append(trace, max(jet[row, "trace"], max(jet[row, "pc"], jet[row, "cv"])))
-    }
-  }
-}else if ((normWeightMode=="maxtracepcsc")|(normWeightMode=="maxtracescpc")){
-  print(paste("Using ", normWeightMode))
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="traceMax")==1){
-      trace<-append(trace, max(jet[row, "traceMax"], max(jet[row, "pc"], jet[row, "clusters"])))
-    }else{
-      trace<-append(trace, max(jet[row, "trace"], max(jet[row, "pc"], jet[row, "clusters"])))
-    }
-  }
-}else if ((normWeightMode=="maxtracehalfpccv")|(normWeightMode=="maxtracehalfcvpc")){
-  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, "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=="maxtracehalftracecvhalfcvpc")){
-  print(paste("Using ", normWeightMode))
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="traceMax")==1){
-      trace<-append(trace, max(jet[row, "traceMax"], max((jet[row, "traceMax"]+jet[row, "cv"])/2.0, (jet[row, "pc"]+jet[row, "cv"])/2.0 )))
-    }else{
-      trace<-append(trace, max(jet[row, "trace"], max((jet[row, "trace"]+jet[row, "cv"])/2.0, (jet[row, "pc"]+jet[row, "cv"])/2.0 )))
-    }
-  }
-}else if ((normWeightMode=="maxhalftracepchalftracecvhalfcvpc")){
+if ((normWeightMode=="maxhalftracepchalftracecvhalfcvpc")){
   print(paste("Using ", normWeightMode))
   for (row in 1:nrow(jet)) {
     if(sum(colnames(jet)=="traceMax")==1){
@@ -136,47 +55,6 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
       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=="jetormax")){
-  print(paste("Using ", normWeightMode))
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="traceMax")==1){
-      maxValue = max((jet[row, "traceMax"]+jet[row, "pc"])/2.0, max((jet[row, "traceMax"]+jet[row, "cv"])/2.0, (jet[row, "pc"]+jet[row, "cv"])/2.0 ))
-      traceValue = jet[row, "traceMax"]
-      trace<-append(trace, max((traceValue), (maxValue)))
-    }else{
-      maxValue = 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 ))
-      traceValue = jet[row, "trace"]
-      trace<-append(trace, max((traceValue), (maxValue)))
-    }
-  }
-}else if ((normWeightMode=="maxtracepchalfpccv")){ 
-  print(paste("Using ", normWeightMode))
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="traceMax")==1){
-      trace<-append(trace, max(jet[row, "traceMax"], max(jet[row, "pc"], (jet[row, "pc"]+jet[row, "cv"])/2.0 )))
-    }else{
-      trace<-append(trace, max(jet[row, "trace"], max(jet[row, "pc"], (jet[row, "pc"]+jet[row, "cv"])/2.0 )   ))
-    }
-  }
-}else if ((normWeightMode=="halfcvpc") | (normWeightMode=="halfpccv")){
-  print(paste("Using ", normWeightMode))
-  for (row in 1:nrow(jet)) {
-    trace<-append(trace, (jet[row, "pc"]+jet[row, "cv"])/2.0)
-    }  
-}else if ((normWeightMode=="halftracepc") | (normWeightMode=="halfpctrace")){
-  print(paste("Using ", normWeightMode))
-  for (row in 1:nrow(jet)) {
-    if(sum(colnames(jet)=="traceMax")==1){
-      trace<-append(trace, (jet[row, "traceMax"]+jet[row, "pc"])/2.0)
-    }else{
-      trace<-append(trace, (jet[row, "trace"]+jet[row, "pc"])/2.0)
-    }
-  }
-} else if ((normWeightMode=="maxcvpc") | (normWeightMode=="maxpccv")){
-  print(paste("Using ", normWeightMode))
-  for (row in 1:nrow(jet)) {
-    trace<-append(trace, max(jet[row, "pc"], jet[row, "cv"]))
-    }  
 }else if (normWeightMode=="trace"){
   print("Using only JET2 traces")
   for (row in 1:nrow(jet)) {
@@ -186,13 +64,6 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
       trace<-append(trace, jet[row, "trace"])
     } 
   }
-}else if (normWeightMode=="tracemovingaverage"){
-  print("Using only tracemovingaverage")
-  for (row in 1:nrow(jet)) {
-    trace<-append(trace, jet[row, "tracemovingaverage"]) 
-  }
-  print("Here is the tracemovingaverage!")
-  print(trace)
 }else if (normWeightMode=="cv"){
   print("Using only CV traces")
   for (row in 1:nrow(jet)) {
@@ -203,16 +74,6 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
   for (row in 1:nrow(jet)) {
     trace<-append(trace, jet[row, "pc"]) 
   }
-}else if (normWeightMode=="dfi"){
-  print("Using only DFI values")
-  for (row in 1:nrow(jet)) {
-    trace<-append(trace, jet[row, "dfi"]) 
-  }
-}else if (normWeightMode=="bfactor"){
-  print("Using only Bfactor values")
-  for (row in 1:nrow(jet)) {
-    trace<-append(trace, jet[row, "bfactor"]) 
-  }
 }else if (normWeightMode=="ssjetormax"){
   print("Using only ssjetormax")
   for (row in 1:nrow(jet)) {
@@ -226,9 +87,8 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
 
 }else{
   print("ERROR: Unknown --normWeightMode selected!")
-  print("It can only be 'trace', 'tracemovingaverage', 'pc', 'cv', 'dfi', 'bfactor',")
-  print(" 'maxtracepc', 'maxtracecv', 'maxtracepccv', 'halfcvpc', 'halftracepc', 'maxtracepchalfpccv',")
-  print(" 'maxtracesc', 'maxtracescpc', 'maxtracedfi', 'maxtracebfactor', 'maxhalftracepchalftracecvhalfcvpc'")
+  print("It can only be 'trace', 'pc', 'cv',")
+  print("'maxhalftracepchalftracecvhalfcvpc'")
   print(" or 'ssjetormax'!")
 }
 print(trace)
@@ -343,8 +203,6 @@ alpha = 0.6
 # }
 #print(alpha)
 
-
-
 #alphabet = "lz-bl.7"
 alphabet = selectedAlphabet
 if(simple){

esgemme.py

@@ -847,38 +847,10 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
     if( (normWeightMode != 'trace') and \
         (normWeightMode != 'cv') and \
         (normWeightMode != 'pc') and \
-        (normWeightMode != 'dfi') and \
-        (normWeightMode != 'bfactor') and \
-        (normWeightMode != 'maxtracepc') and \
-        (normWeightMode != 'maxpctrace') and \
-        (normWeightMode != 'maxpccv') and \
-        (normWeightMode != 'maxcvpc') and \
-        (normWeightMode != 'maxtracecv') and \
-        (normWeightMode != 'maxtracesc') and \
-        (normWeightMode != 'maxcvtrace') and \
-        (normWeightMode != 'maxtracedfi') and \
-        (normWeightMode != 'maxtracebfactor') and \
-        (normWeightMode != 'maxdfitrace') and \
-        (normWeightMode != 'maxbfactortrace') and \
-        (normWeightMode != 'maxtracepccv') and \
-        (normWeightMode != 'maxtracepcsc') and \
-        (normWeightMode != 'maxtracepchalfpccv') and \
-        (normWeightMode != 'maxtracecvpc') and \
-        (normWeightMode != 'halfpccv') and \
-        (normWeightMode != 'halfcvpc') and \
-        (normWeightMode != 'halftracepc') and \
-        (normWeightMode != 'maxtracehalfcvpc') and \
-        (normWeightMode != 'maxtracehalftracecvhalfcvpc') and \
         (normWeightMode != 'maxhalftracepchalftracecvhalfcvpc') and \
-        (normWeightMode != 'jetormax') and \
-        (normWeightMode != 'ssjetormax') and \
-        (normWeightMode != 'tracemovingaverage') and \
-        (normWeightMode != 'maxtracehalfpccv')):
-        print("ERROR: normWeightMode can only be 'trace', 'tracemovingaverage', 'cv', 'pc', 'dfi', bfactor,\n"+\
-              "       'maxtracepc', 'maxtracedfi', 'maxpccv', 'maxtracesc',"+\
-              "       'maxtracebfactor', 'maxtracepcsc', 'maxhalftracepchalftracecvhalfcvpc', "+\
-              "       'maxtracecv', 'maxtracepccv', maxtracepchalfpccv"+\
-              "       'halfcvpc', 'halftracepc', 'maxtracehalfcvpc', 'maxtracehalftracecvhalfcvpc' or 'ssjetormax'!")
+        (normWeightMode != 'ssjetormax')):
+        print("ERROR: normWeightMode can only be 'trace', 'cv', 'pc', "+\
+              "'maxhalftracepchalftracecvhalfcvpc' or 'ssjetormax'!")
         sys.exit(-1)
 
     structure = parsePDB(prot+".pdb")