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Commit 8f6e1b64 by Mustafa Tekpinar
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Moved editConf and launchJET from gemmeAnal.py to sgemme.py

parent 9f20b4c1
Showing with 369 additions and 171 deletions
gemmeAnal.py
...@@ -73,201 +73,201 @@ import numpy as np ...@@ -73,201 +73,201 @@ import numpy as np
# fOUT.close() # fOUT.close()
def editConfJET(N): # def editConfJET(N):
""" # """
# Edit JET configuration file with correct number of Seqs & MSA # # Edit JET configuration file with correct number of Seqs & MSA
""" # """
reCode=subprocess.call("sed -i 's/results\t\t5000/results\t\t"+str(N)+"/' default.conf",shell=True) # reCode=subprocess.call("sed -i 's/results\t\t5000/results\t\t"+str(N)+"/' default.conf",shell=True)
return(reCode) # return(reCode)
def minMaxNormalization(data): # def minMaxNormalization(data):
""" # """
Min-max normalization of a data array. # Min-max normalization of a data array.
""" # """
return (data - np.min(data)) / (np.max(data) - np.min(data)) # return (data - np.min(data)) / (np.max(data) - np.min(data))
# Run JET to compute TJET values # # Run JET to compute TJET values
def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): # def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
""" # """
Call JET2 and produce prot+"_jet.res" file. # Call JET2 and produce prot+"_jet.res" file.
prot+"_jet.res" will be used in the following steps (in launchPred) # prot+"_jet.res" will be used in the following steps (in launchPred)
to calculate independent and epistatic models. # to calculate independent and epistatic models.
Ideally, this call to JET2 should be from Dockers or Singularity # Ideally, this call to JET2 should be from Dockers or Singularity
because installing all requirements of JET2 is a pain in the ass! # because installing all requirements of JET2 is a pain in the ass!
Parameters # Parameters
---------- # ----------
prot: string ??? # prot: string ???
Name of the protein ??? # Name of the protein ???
retMet: string # retMet: string
Retreival method of multiple sequence alignments file # Retreival method of multiple sequence alignments file
It can be 'input', 'local' or 'server'. Default is local. # It can be 'input', 'local' or 'server'. Default is local.
bFile: string # bFile: string
A multiple sequence alignment file obtained with psiblast. # A multiple sequence alignment file obtained with psiblast.
It is used only if the retMet (explained above) is input. # It is used only if the retMet (explained above) is input.
fFile: string # fFile: string
A multiple sequence alignment file obtained with psiblast. # A multiple sequence alignment file obtained with psiblast.
It is used only if the retMet (explained above) is input. # It is used only if the retMet (explained above) is input.
pdbfile: string # pdbfile: string
a Protein Data Bank file obtained with rcsb.org or any # a Protein Data Bank file obtained with rcsb.org or any
computational method like alphafold. # computational method like alphafold.
If it is None, only JET and PC scores are calculated. # If it is None, only JET and PC scores are calculated.
Otherwise, CV and other structural-dynamical features also # Otherwise, CV and other structural-dynamical features also
can be calculated. # can be calculated.
chains: list # chains: list
A list of chains available in the pdb file. # A list of chains available in the pdb file.
Most of the time, it is supposed to be just one! # Most of the time, it is supposed to be just one!
n: int # n: int
Number of JET2 iterations. # Number of JET2 iterations.
N: int # N: int
Default 40000 # Default 40000
nl: int # nl: int
Number of lines after > character in the query sequences file. # Number of lines after > character in the query sequences file.
It is obtained in extractQuerySeq() function. # It is obtained in extractQuerySeq() function.
Returns # Returns
------- # -------
Nothing # Nothing
""" # """
chainID = chains[0] # chainID = chains[0]
#TODO: Remove Bash dependency here. Make the copying process in Python # #TODO: Remove Bash dependency here. Make the copying process in Python
subprocess.call("cp $SGEMME_PATH/default.conf .",shell=True) # subprocess.call("cp $SGEMME_PATH/default.conf .",shell=True)
if retMet=="input": # if retMet=="input":
if bFile!='': # if bFile!='':
#TODO: I think these two lines must be here as well but I am not sure. # #TODO: I think these two lines must be here as well but I am not sure.
# print(N) # # print(N)
# editConfJET(N) # # editConfJET(N)
if(bFile == prot+"_"+chainID+".psiblast"): # if(bFile == prot+"_"+chainID+".psiblast"):
shutil.copy2(bFile, bFile+".orig") # shutil.copy2(bFile, bFile+".orig")
shutil.copy2(bFile+".orig ", prot+"_"+chainID+".psiblast") # shutil.copy2(bFile+".orig ", prot+"_"+chainID+".psiblast")
else: # else:
shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast") # shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast")
if(pdbfile == None): # if(pdbfile == None):
jetcmd = "java -Xmx4096m -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 -Xmx4096m -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 -Xmx4096m -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'
else: # else:
print(N) # print(N)
editConfJET(N) # editConfJET(N)
if(fFile == prot+"_"+chainID+".fasta"): # if(fFile == prot+"_"+chainID+".fasta"):
shutil.copy2(fFile, fFile+".orig") # shutil.copy2(fFile, fFile+".orig")
#I think this subprocess call causes overwriting of the fasta file. # #I think this subprocess call causes overwriting of the fasta file.
#subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True) # #subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True)
grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+".orig > "+prot+"_"+chainID+".fasta" # grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+".orig > "+prot+"_"+chainID+".fasta"
else: # else:
#subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True) # #subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True)
grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+" > "+prot+"_"+chainID+".fasta" # grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+" > "+prot+"_"+chainID+".fasta"
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 -Xmx4096m -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"
print("\nRunning command:\n"+jetcmd) # print("\nRunning command:\n"+jetcmd)
reCode=subprocess.call(jetcmd,shell=True) # reCode=subprocess.call(jetcmd,shell=True)
if os.path.isfile(prot+"/"+prot+"_jet.res"): # if os.path.isfile(prot+"/"+prot+"_jet.res"):
os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res") # os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
else: # else:
# Calculate SC1 # # Calculate SC1
jetcmd = "java -Xmx4096m -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 3"+" > "+prot+".out" # prot+".pdb -o `pwd` -p AVJCG -r input -f "+prot+"_"+chainID+".fasta -d chain -n "+n+" -a 3"+" > "+prot+".out"
#One can also add: -g 'trace,pc,cv,clusters,axs' # #One can also add: -g 'trace,pc,cv,clusters,axs'
print("\nRunning for SC1:\n"+jetcmd) # print("\nRunning for SC1:\n"+jetcmd)
reCode=subprocess.call(jetcmd,shell=True) # reCode=subprocess.call(jetcmd,shell=True)
if os.path.isfile(prot+"/"+prot+"_jet.res"): # if os.path.isfile(prot+"/"+prot+"_jet.res"):
os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res") # os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
dir_name = prot+"/" # dir_name = prot+"/"
if os.path.isdir(dir_name): # if os.path.isdir(dir_name):
for f in os.listdir(dir_name): # for f in os.listdir(dir_name):
f_path = os.path.join(dir_name, f) # f_path = os.path.join(dir_name, f)
if os.path.isfile(f_path): # if os.path.isfile(f_path):
os.remove(f_path) # os.remove(f_path)
os.rmdir(dir_name) # os.rmdir(dir_name)
else: # else:
if(pdbfile == None): # if(pdbfile == None):
jetcmd = "java -Xmx4096m -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 -Xmx4096m -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 -Xmx4096m -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"
reCode=subprocess.call(jetcmd,shell=True) # reCode=subprocess.call(jetcmd,shell=True)
if os.path.isfile(prot+"/"+prot+"_jet.res"): # if os.path.isfile(prot+"/"+prot+"_jet.res"):
os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res") # os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
dir_name = prot+"/" # dir_name = prot+"/"
if os.path.isdir(dir_name): # if os.path.isdir(dir_name):
for f in os.listdir(dir_name): # for f in os.listdir(dir_name):
f_path = os.path.join(dir_name, f) # f_path = os.path.join(dir_name, f)
if os.path.isfile(f_path): # if os.path.isfile(f_path):
os.remove(f_path) # os.remove(f_path)
os.rmdir(dir_name) # os.rmdir(dir_name)
# print("\nRunning:\n"+jetcmd) # # print("\nRunning:\n"+jetcmd)
# reCode=subprocess.call(jetcmd,shell=True) # # reCode=subprocess.call(jetcmd,shell=True)
# if os.path.isfile(prot+"/"+prot+"_jet.res"): # # if os.path.isfile(prot+"/"+prot+"_jet.res"):
# os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res") # # os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
return(reCode) # return(reCode)
# Run Rscript to compute predictions # # Run Rscript to compute predictions
def launchPred(prot,inAli,mutFile, normWeightMode, alphabet): # def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
if mutFile!='': # if mutFile!='':
rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet # rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
else: # else:
rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet # rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
print("\nRunning: \n"+rcmd) # print("\nRunning: \n"+rcmd)
reCode=subprocess.call(rcmd,shell=True) # reCode=subprocess.call(rcmd,shell=True)
#Add plots here with gemmemore # #Add plots here with gemmemore
return(reCode) # return(reCode)
# Remove temporary files # # Remove temporary files
def cleanTheMess(prot,bFile,fFile, chainID): # def cleanTheMess(prot,bFile,fFile, chainID):
if bFile!='': # if bFile!='':
if bFile!=prot+"_"+chainID+".psiblast": # if bFile!=prot+"_"+chainID+".psiblast":
os.remove(prot+"_"+chainID+".psiblast") # os.remove(prot+"_"+chainID+".psiblast")
else: # else:
if os.path.isfile(prot+"/"+prot+"_"+chainID+".psiblast"): # if os.path.isfile(prot+"/"+prot+"_"+chainID+".psiblast"):
os.rename(prot+"/"+prot+"_"+chainID+".psiblast",prot+"_"+chainID+".psiblast") # os.rename(prot+"/"+prot+"_"+chainID+".psiblast",prot+"_"+chainID+".psiblast")
if fFile!='': # if fFile!='':
if fFile!=prot+"_"+chainID+".fasta": # if fFile!=prot+"_"+chainID+".fasta":
if os.path.isfile(prot+"_"+chainID+".fasta"): # if os.path.isfile(prot+"_"+chainID+".fasta"):
os.remove(prot+"_"+chainID+".fasta") # os.remove(prot+"_"+chainID+".fasta")
# if os.path.isfile(prot+"/"+prot+"_jet.res"): # # if os.path.isfile(prot+"/"+prot+"_jet.res"):
# os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res") # # os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
# os.remove(prot+".pdb") # # os.remove(prot+".pdb")
# Get all files with suffix nwk # # Get all files with suffix nwk
treefiles = glob.glob('*.nwk') # treefiles = glob.glob('*.nwk')
# Iterate over the list of files and remove individually # # Iterate over the list of files and remove individually
for file in treefiles: # for file in treefiles:
os.remove(file) # os.remove(file)
dir_name = prot+"/" # dir_name = prot+"/"
if os.path.isdir(dir_name): # if os.path.isdir(dir_name):
for f in os.listdir(dir_name): # for f in os.listdir(dir_name):
f_path = os.path.join(dir_name, f) # f_path = os.path.join(dir_name, f)
if os.path.isfile(f_path): # if os.path.isfile(f_path):
os.remove(f_path) # os.remove(f_path)
os.rmdir(dir_name) # os.rmdir(dir_name)
sgemme.py
...@@ -78,6 +78,204 @@ def createPDB(prot,seq): ...@@ -78,6 +78,204 @@ def createPDB(prot,seq):
i += 1 i += 1
fOUT.close() fOUT.close()
def editConfJET(N):
"""
# Edit JET configuration file with correct number of Seqs & MSA
"""
reCode=subprocess.call("sed -i 's/results\t\t5000/results\t\t"+str(N)+"/' default.conf",shell=True)
return(reCode)
def minMaxNormalization(data):
"""
Min-max normalization of a data array.
"""
return (data - np.min(data)) / (np.max(data) - np.min(data))
# Run JET to compute TJET values
def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
"""
Call JET2 and produce prot+"_jet.res" file.
prot+"_jet.res" will be used in the following steps (in launchPred)
to calculate independent and epistatic models.
Ideally, this call to JET2 should be from Dockers or Singularity
because installing all requirements of JET2 is a pain in the ass!
Parameters
----------
prot: string ???
Name of the protein ???
retMet: string
Retreival method of multiple sequence alignments file
It can be 'input', 'local' or 'server'. Default is local.
bFile: string
A multiple sequence alignment file obtained with psiblast.
It is used only if the retMet (explained above) is input.
fFile: string
A multiple sequence alignment file obtained with psiblast.
It is used only if the retMet (explained above) is input.
pdbfile: string
a Protein Data Bank file obtained with rcsb.org or any
computational method like alphafold.
If it is None, only JET and PC scores are calculated.
Otherwise, CV and other structural-dynamical features also
can be calculated.
chains: list
A list of chains available in the pdb file.
Most of the time, it is supposed to be just one!
n: int
Number of JET2 iterations.
N: int
Default 40000
nl: int
Number of lines after > character in the query sequences file.
It is obtained in extractQuerySeq() function.
Returns
-------
Nothing
"""
chainID = chains[0]
#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.
# print(N)
# editConfJET(N)
if(bFile == prot+"_"+chainID+".psiblast"):
shutil.copy2(bFile, bFile+".orig")
shutil.copy2(bFile+".orig ", prot+"_"+chainID+".psiblast")
else:
shutil.copy2(bFile+" ", prot+"_"+chainID+".psiblast")
if(pdbfile == None):
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"
else:
# 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"
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"
#One can also add: -g 'trace,pc,cv,clusters,axs'
else:
print(N)
editConfJET(N)
if(fFile == prot+"_"+chainID+".fasta"):
shutil.copy2(fFile, fFile+".orig")
#I think this subprocess call causes overwriting of the fasta file.
#subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True)
grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+".orig > "+prot+"_"+chainID+".fasta"
else:
#subprocess.call("cp "+fFile+" "+prot+"_"+chainID+".fasta",shell=True)
grpcmd="grep -m "+str(int(N)+1)+" -A "+str(nl)+" '^>' "+fFile+" > "+prot+"_"+chainID+".fasta"
print("\nRunning:\n"+grpcmd)
subprocess.call(grpcmd,shell=True)
if(pdbfile == None):
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"
print("\nRunning command:\n"+jetcmd)
reCode=subprocess.call(jetcmd,shell=True)
if os.path.isfile(prot+"/"+prot+"_jet.res"):
os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
else:
# Calculate SC1
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 3"+" > "+prot+".out"
#One can also add: -g 'trace,pc,cv,clusters,axs'
print("\nRunning for SC1:\n"+jetcmd)
reCode=subprocess.call(jetcmd,shell=True)
if os.path.isfile(prot+"/"+prot+"_jet.res"):
os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
dir_name = prot+"/"
if os.path.isdir(dir_name):
for f in os.listdir(dir_name):
f_path = os.path.join(dir_name, f)
if os.path.isfile(f_path):
os.remove(f_path)
os.rmdir(dir_name)
else:
if(pdbfile == None):
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"
else:
# 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"
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"
reCode=subprocess.call(jetcmd,shell=True)
if os.path.isfile(prot+"/"+prot+"_jet.res"):
os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
dir_name = prot+"/"
if os.path.isdir(dir_name):
for f in os.listdir(dir_name):
f_path = os.path.join(dir_name, f)
if os.path.isfile(f_path):
os.remove(f_path)
os.rmdir(dir_name)
# print("\nRunning:\n"+jetcmd)
# reCode=subprocess.call(jetcmd,shell=True)
# if os.path.isfile(prot+"/"+prot+"_jet.res"):
# os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
return(reCode)
# Run Rscript to compute predictions
def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
if mutFile!='':
rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" FALSE "+mutFile+" "+normWeightMode+" "+alphabet
else:
rcmd="Rscript --save $SGEMME_PATH/computePred.R "+prot+" "+inAli+" TRUE none "+normWeightMode+" "+alphabet
print("\nRunning: \n"+rcmd)
reCode=subprocess.call(rcmd,shell=True)
#Add plots here with gemmemore
return(reCode)
# Remove temporary files
def cleanTheMess(prot,bFile,fFile, chainID):
if bFile!='':
if bFile!=prot+"_"+chainID+".psiblast":
os.remove(prot+"_"+chainID+".psiblast")
else:
if os.path.isfile(prot+"/"+prot+"_"+chainID+".psiblast"):
os.rename(prot+"/"+prot+"_"+chainID+".psiblast",prot+"_"+chainID+".psiblast")
if fFile!='':
if fFile!=prot+"_"+chainID+".fasta":
if os.path.isfile(prot+"_"+chainID+".fasta"):
os.remove(prot+"_"+chainID+".fasta")
# if os.path.isfile(prot+"/"+prot+"_jet.res"):
# os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
# os.remove(prot+".pdb")
# Get all files with suffix nwk
treefiles = glob.glob('*.nwk')
# Iterate over the list of files and remove individually
for file in treefiles:
os.remove(file)
dir_name = prot+"/"
if os.path.isdir(dir_name):
for f in os.listdir(dir_name):
f_path = os.path.join(dir_name, f)
if os.path.isfile(f_path):
os.remove(f_path)
os.rmdir(dir_name)
############################################################################### ###############################################################################
def rankSortProteinData(dataArray, inverted=True): def rankSortProteinData(dataArray, inverted=True):
......
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