modifying script to avoid invoking bash as a subprocess
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fab1fb0492
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1 changed files with 29 additions and 2 deletions
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@ -195,6 +195,19 @@ def loadFiles(df):
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f.close()
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return np.asarray(resultList, dtype=np.float32)
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# TODO: use this code pattern rather than invoking bash
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#def repairPDB():
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# subprocess.call(['foldx'
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# , '--command=RepairPDB'
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# , '--pdb-dir=' + indir
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# , '--pdb=' + actual_pdb_filename
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# , '--ionStrength=0.05'#
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# , '--pH=7'
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# , '--water=PREDICT'
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# , '--vdwDesign=1'
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# , 'outPDB=true'
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# , '--output-dir=' + process_dir])
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#=======================================================================
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def main():
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pdbname = pdb_name
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@ -210,7 +223,19 @@ def main():
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#subprocess.check_output(['bash','repairPDB.sh', pdbname, process_dir])
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print('\033[95mSTAGE: repair PDB\033[0m')
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print('EXECUTING: repairPDB.sh %s %s %s' % (indir, actual_pdb_filename, process_dir))
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subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
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#subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
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# once you decide to use the function
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# repairPDB(pdbname)
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subprocess.call(['foldx'
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, '--command=RepairPDB'
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, '--pdb-dir=' + indir
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, '--pdb=' + actual_pdb_filename
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, '--ionStrength=0.05'#
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, '--pH=7'
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, '--water=PREDICT'
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, '--vdwDesign=1'
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, 'outPDB=true'
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, '--output-dir=' + process_dir])
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print('\033[95mCOMPLETE: repair PDB\033[0m')
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print('\033[95mSTAGE: run FoldX (shell)\033[0m')
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print('EXECUTING: runfoldx.sh %s %s ' % (pdbname, process_dir))
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@ -242,7 +267,9 @@ def main():
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chain1=chainA
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chain2=chainB
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with suppress(Exception):
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subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir])
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#subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir])
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subprocess(['foldx --command=AnalyseComplex --pdb="%s_Repair.pdb" --analyseComplexChains=%s,%s --water=PREDICT --vdwDesign=1 --output-dir=%s'] % (pdbname, chain1, chain2, process_dir))
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for n in range(1,nmuts+1):
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print('\033[95mSTAGE: Run Mutation Complex (shell) for mutation:\033[0m', n)
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with suppress(Exception):
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