Added jetormax to the normalization options

computePred.R

 # Copyright (c) 2018: Elodie Laine
-# Copyright (c) 2022: Mustafa Tekpinar
+# Copyright (c) 2022-2023: Mustafa Tekpinar
 # This code is part of the gemme package and governed by its license.
 # Please see the LICENSE.txt file included as part of this package.
 
 # Usage: Rscript --save computePred.R XXXX
 
 library("seqinr")
-source(paste(Sys.getenv("GEMME_PATH"),"/pred.R",sep=""))
+source(paste(Sys.getenv("SGEMME_PATH"),"/pred.R",sep=""))
 
 # amino acid full alphabet
 aa = c("a","c","d","e","f","g","h","i","k","l","m","n","p","q","r","s","t","v","w","y")
 
 # BLOSUM62  matrix
-blosum62p = as.matrix(read.table(paste0(Sys.getenv("GEMME_PATH"),"/blosum62p.txt"),row.names=1))
+blosum62p = as.matrix(read.table(paste0(Sys.getenv("SGEMME_PATH"),"/blosum62p.txt"),row.names=1))
 bgp = blosum62p[order(rownames(blosum62p)),order(colnames(blosum62p))]
 bg = apply(bgp,1,sum)
 
@@ -136,6 +136,19 @@ 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)) {
@@ -244,7 +257,8 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
   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' or 'maxtracebfactor'!")
+  print(" 'maxtracesc', 'maxtracescpc', 'maxtracedfi', 'maxtracebfactor', 'maxhalftracepchalftracecvhalfcvpc'")
+  print(" or 'jetormax'!")
 }
 print(trace)
 #####################################################################################################################

gemmeAnal.py

@@ -16,30 +16,30 @@ import pandas as pd
 import numpy as np
 
 
-
-def extractQuerySeq(filename):
-	"""
-		# Extract the query sequence from the input alignment
-	"""
-
-	fIN = open(filename,"r")
-	lines = fIN.readlines()
-	fIN.close()
-
-	if lines[0][0]!=">":
-		raise Exception('bad FASTA format')
-	else:
-		prot = re.compile("[^A-Z0-9a-z]").split(lines[0][1:])[0]
-		fOUT = open(prot+".fasta","w")
-		fOUT.write(">"+prot+"\n")
-		seq=""
-		i = 1
-		while lines[i][0]!=">":
-			seq = seq + lines[i].strip().strip(".").strip("-")
-			fOUT.write(lines[i])
-			i = i + 1
-	fOUT.close()
-	return prot,seq,i-1
+# Moved to sgemme.py
+# def extractQuerySeq(filename):
+# 	"""
+# 		# Extract the query sequence from the input alignment
+# 	"""
+
+# 	fIN = open(filename,"r")
+# 	lines = fIN.readlines()
+# 	fIN.close()
+
+# 	if lines[0][0]!=">":
+# 		raise Exception('bad FASTA format')
+# 	else:
+# 		prot = re.compile("[^A-Z0-9a-z]").split(lines[0][1:])[0]
+# 		fOUT = open(prot+".fasta","w")
+# 		fOUT.write(">"+prot+"\n")
+# 		seq=""
+# 		i = 1
+# 		while lines[i][0]!=">":
+# 			seq = seq + lines[i].strip().strip(".").strip("-")
+# 			fOUT.write(lines[i])
+# 			i = i + 1
+# 	fOUT.close()
+# 	return prot,seq,i-1
 
 
 def getNbSeq(filename):
@@ -135,7 +135,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
 	
 	#TODO: Remove Bash dependency here. Make the copying process in Python
 	subprocess.call("cp $SGEMME_PATH/default.conf .",shell=True)
-	
+
 	if retMet=="input":
 		if bFile!='':
 			#TODO: I think these two lines must be here as well but I am not sure. 

pred.R

@@ -174,7 +174,7 @@ computePSSM2<-function(mat){
 }
 
 computeNbSeqsAlph<-function(nbSeqs,alphabet){
-	path=paste(Sys.getenv("GEMME_PATH"),"/alphabets/",sep="")
+	path=paste(Sys.getenv("SGEMME_PATH"),"/alphabets/",sep="")
         AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
         facAA = rep(NA,20)
         for(Let in AA){
@@ -210,7 +210,7 @@ readMut<-function(fname){
 }
 
 which.class<-function(a,alphabet){
-        path=paste(Sys.getenv("GEMME_PATH"),"/alphabets/",sep="")
+        path=paste(Sys.getenv("SGEMME_PATH"),"/alphabets/",sep="")
         AA = read.table(paste(path,alphabet,".txt",sep=""))$V1
         for(Let in AA){
                 Let = toString(Let)

sgemme.py

@@ -22,6 +22,8 @@ from gemmeAnal import *
 
 import pandas as pd
 
+#############The following part between # signs are moved from gemmeAnal.py to 
+# make the code more simple.  
 def extractQuerySeq(filename):
 	"""
 		# Extract the query sequence from the input alignment
@@ -45,7 +47,7 @@ def extractQuerySeq(filename):
 			i = i + 1
 	fOUT.close()
 	return prot,seq,i-1
-
+###############################################################################
 def rankSortProteinData(dataArray, inverted=True):
     """
         This function ranksorts protein data and converts it
@@ -477,7 +479,8 @@ def parse_command_line():
     
     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' or 'halfcvpc'. Default is 'trace'.",
+            "'maxtracepc', 'maxtracecv', 'maxtracepccv', 'maxtracepcsc', 'maxtracepchalfpccv', "+\
+            "'halfcvpc', maxhalftracepchalftracecvhalfcvpc or jetormax. Default is 'trace'.",
         required=False, default="trace")
 
     args = parser.parse_args()
@@ -548,6 +551,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
         (normWeightMode != 'maxtracehalfcvpc') and \
         (normWeightMode != 'maxtracehalftracecvhalfcvpc') and \
         (normWeightMode != 'maxhalftracepchalftracecvhalfcvpc') and \
+        (normWeightMode != 'jetormax') and \
         (normWeightMode != 'tracemovingaverage') and \
         (normWeightMode != 'maxtracehalfpccv')):
         print("ERROR: normWeightMode can only be 'trace', 'tracemovingaverage', 'cv', 'pc', 'dfi', bfactor,\n"+\
@@ -555,7 +559,7 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
               "       'maxtracebfactor', 'maxtracepcsc', 'maxhalftracepchalftracecvhalfcvpc', "+\
               "       'maxtracecv', 'maxtracepccv', maxtracepchalfpccv"+\
               "       'combinedv1', 'combinedv2', 'combinedv3', 'combinedv4'"+\
-              "       'halfcvpc', 'halftracepc', 'maxtracehalfcvpc' or maxtracehalftracecvhalfcvpc!")
+              "       'halfcvpc', 'halftracepc', 'maxtracehalfcvpc', 'maxtracehalftracecvhalfcvpc' or 'jetormax'!")
         sys.exit(-1)
 
     structure = parsePDB(prot+".pdb")