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Commit f469ecb8 by Mustafa Tekpinar
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Changed default.conf file copy process from bash to more Pythonic way.

parent b20bee53
Showing with 6 additions and 1 deletions
esgemme.py
...@@ -173,7 +173,11 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): ...@@ -173,7 +173,11 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
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 $ESGEMME_PATH/default.conf .",shell=True) #subprocess.call("cp $ESGEMME_PATH/default.conf .",shell=True)
esgemme_path = os.path.expandvars ('$ESGEMME_PATH')
shutil.copy2(os.path.join(esgemme_path, "default.conf"), os.getcwd())
if retMet=="input": if retMet=="input":
if bFile!='': if bFile!='':
...@@ -186,6 +190,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl): ...@@ -186,6 +190,7 @@ def launchJET(prot, retMet, bFile, fFile, pdbfile, chains, n, N, nl):
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"
......
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