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Commit 93c7e057 by Mustafa Tekpinar
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Some new combinations of JET. 

Added maxhalftracepchalftracecvhalfcvpc maxtracehalftracecvhalfcvpc. In addition, increased java memory request from -Xmx2048m to -Xmx4096m.
parent d30ef32b
Showing with 32 additions and 12 deletions
computePred.R
...@@ -118,6 +118,24 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){ ...@@ -118,6 +118,24 @@ if((normWeightMode=="maxtracepc") | (normWeightMode=="maxpctrace")){
trace<-append(trace, max(jet[row, "trace"], (jet[row, "pc"]+jet[row, "cv"])/2.0 )) 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")){
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"])/2.0, 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"]+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=="maxtracepchalfpccv")){ }else if ((normWeightMode=="maxtracepchalfpccv")){
print(paste("Using ", normWeightMode)) print(paste("Using ", normWeightMode))
for (row in 1:nrow(jet)) { for (row in 1:nrow(jet)) {
......
gemme.py
...@@ -516,13 +516,15 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode, ...@@ -516,13 +516,15 @@ def doit(inAli,mutFile,retMet,bFile,fFile,n,N, jetfile, pdbfile, normWeightMode,
(normWeightMode != 'halfpccv') and \ (normWeightMode != 'halfpccv') and \
(normWeightMode != 'halfcvpc') and \ (normWeightMode != 'halfcvpc') and \
(normWeightMode != 'maxtracehalfcvpc') and \ (normWeightMode != 'maxtracehalfcvpc') and \
(normWeightMode != 'maxtracehalftracecvhalfcvpc') and \
(normWeightMode != 'maxhalftracepchalftracecvhalfcvpc') and \
(normWeightMode != 'tracemovingaverage') and \ (normWeightMode != 'tracemovingaverage') and \
(normWeightMode != 'maxtracehalfpccv')): (normWeightMode != 'maxtracehalfpccv')):
print("ERROR: normWeightMode can only be 'trace', 'tracemovingaverage', 'cv', 'pc', 'dfi', bfactor,\n"+\ print("ERROR: normWeightMode can only be 'trace', 'tracemovingaverage', 'cv', 'pc', 'dfi', bfactor,\n"+\
" 'maxtracepc', 'maxtracedfi', 'maxpccv', 'maxtracesc',"+\ " 'maxtracepc', 'maxtracedfi', 'maxpccv', 'maxtracesc',"+\
" 'maxtracebfactor', 'maxtracepcsc', "+\ " 'maxtracebfactor', 'maxtracepcsc', 'maxhalftracepchalftracecvhalfcvpc', "+\
" 'maxtracecv', 'maxtracepccv', maxtracepchalfpccv"+\ " 'maxtracecv', 'maxtracepccv', maxtracepchalfpccv"+\
" 'halfcvpc' or maxtracehalfcvpc!") " 'halfcvpc', 'maxtracehalfcvpc' or maxtracehalftracecvhalfcvpc!")
sys.exit(-1) sys.exit(-1)
structure = parsePDB(prot+".pdb") structure = parsePDB(prot+".pdb")
......
gemmeAnal.py
...@@ -64,7 +64,7 @@ def createPDB(prot,seq): ...@@ -64,7 +64,7 @@ def createPDB(prot,seq):
i = 1 i = 1
for let in seq: for let in seq:
if(let != '-'): if(let != '-'):
fOUT.write('ATOM%7d CA %s A%4d 43.524 70.381 46.465 1.00 0.0\n'%(i,d[let],i)) fOUT.write('ATOM%7d CA %s A%4d 43.524 70.381 46.465 1.00 0.0\n'%(i,d[let.upper()],i))
i += 1 i += 1
fOUT.close() fOUT.close()
...@@ -136,12 +136,12 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): ...@@ -136,12 +136,12 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
else: else:
shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast") shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast")
if(pdbfile == None): if(pdbfile == None):
jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
prot+".pdb -o `pwd` -p J -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out" prot+".pdb -o `pwd` -p J -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out"
else: else:
# jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ # jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# prot+".pdb -o `pwd` -p AVJ -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out" # prot+".pdb -o `pwd` -p AVJ -r input -b "+prot+"_"+chainID+".psiblast -d chain -n "+n+" > "+prot+".out"
jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".psiblast -d chain -n "+n+" -a 5"+" > "+prot+".out" prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".psiblast -d chain -n "+n+" -a 5"+" > "+prot+".out"
#One can also add: -g 'trace,pc,cv,clusters,axs' #One can also add: -g 'trace,pc,cv,clusters,axs'
...@@ -161,22 +161,22 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): ...@@ -161,22 +161,22 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
print("\nRunning:\n"+grpcmd) print("\nRunning:\n"+grpcmd)
subprocess.call(grpcmd,shell=True) subprocess.call(grpcmd,shell=True)
if(pdbfile == None): if(pdbfile == None):
jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
prot+".pdb -o `pwd` -p J -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" > "+prot+".out" prot+".pdb -o `pwd` -p J -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" > "+prot+".out"
else: else:
# jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ # jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# prot+".pdb -o `pwd` -p AVJ -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" > "+prot+".out" # prot+".pdb -o `pwd` -p AVJ -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" > "+prot+".out"
jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" -a 5"+" > "+prot+".out" prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" -a 5"+" > "+prot+".out"
#One can also add: -g 'trace,pc,cv,clusters,axs' #One can also add: -g 'trace,pc,cv,clusters,axs'
else: else:
if(pdbfile == None): if(pdbfile == None):
jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
prot+".pdb -o `pwd` -p J -r "+retMet+" -d chain -n "+n+" > "+prot+".out" prot+".pdb -o `pwd` -p J -r "+retMet+" -d chain -n "+n+" > "+prot+".out"
else: else:
# jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ # jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
# prot+".pdb -o `pwd` -p AVJ -r "+retMet+" -d chain -n "+n+" > "+prot+".out" # prot+".pdb -o `pwd` -p AVJ -r "+retMet+" -d chain -n "+n+" > "+prot+".out"
jetcmd = "java -Xmx2048m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\ jetcmd = "java -Xmx4096m -cp $JET2_PATH:$JET2_PATH/jet/extLibs/vecmath.jar jet.JET -c default.conf -i "+\
prot+".pdb -o `pwd` -p AVJCG -r "+retMet+" -d chain -n "+n+" -a 5"+" > "+prot+".out" prot+".pdb -o `pwd` -p AVJCG -r "+retMet+" -d chain -n "+n+" -a 5"+" > "+prot+".out"
print("\nRunning:\n"+jetcmd) print("\nRunning:\n"+jetcmd)
reCode=subprocess.call(jetcmd,shell=True) reCode=subprocess.call(jetcmd,shell=True)
......
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