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remove shell scripts run with subprocess() and launch foldx directly from python

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This commit is contained in:
Tanushree Tunstall 2021-02-08 18:06:02 +00:00
parent 9df3913a84
commit 86670bbac3
6 changed files with 86 additions and 17 deletions
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0
foldx/test2/mutruncomplex.sh → foldx/test2/deprecated_shell/mutruncomplex.sh
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foldx/test2/repairPDB.sh → foldx/test2/deprecated_shell/repairPDB.sh
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foldx/test2/runPrintNetworks.sh → foldx/test2/deprecated_shell/runPrintNetworks.sh
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foldx/test2/runcomplex.sh → foldx/test2/deprecated_shell/runcomplex.sh
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foldx/test2/runfoldx.sh → foldx/test2/deprecated_shell/runfoldx.sh
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103
foldx/test2/runFoldx.py
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@ -9,6 +9,7 @@ from pathlib import Path
import re
import csv
import argparse
import shutil
#https://realpython.com/python-pathlib/
# FIXME
@ -226,55 +227,123 @@ def main():
#subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
# once you decide to use the function
# repairPDB(pdbname)
# FIXME: put this hack elsewhere
foldx_common=' --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 '
subprocess.call(['foldx'
, '--command=RepairPDB'
, foldx_common
, '--pdb-dir=' + indir
, '--pdb=' + actual_pdb_filename
, '--ionStrength=0.05'#
, '--pH=7'
, '--water=PREDICT'
, '--vdwDesign=1'
, 'outPDB=true'
, '--output-dir=' + process_dir])
print('\033[95mCOMPLETE: repair PDB\033[0m')
print('\033[95mSTAGE: run FoldX (shell)\033[0m')
print('\033[95mSTAGE: run FoldX (subprocess)\033[0m')
print('EXECUTING: runfoldx.sh %s %s ' % (pdbname, process_dir))
output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir])
print('\033[95mCOMPLETE: run FoldX (shell)\033[0m')
#output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir])
print('Running foldx BuildModel')
subprocess.call(['foldx'
, '--command=BuildModel'
, foldx_common
, '--pdb-dir=' + process_dir
, '--pdb=' + pdbname + '_Repair.pdb'
, '--mutant-file="individual_list_' + pdbname +'.txt"'
, 'outPDB=true'
, '--numberOfRuns=1'
, '--output-dir=' + process_dir], cwd=process_dir)
print('Running foldx PrintNetworks')
subprocess.call(['foldx'
, '--command=PrintNetworks'
, '--pdb-dir=' + process_dir
, '--pdb=' + pdbname + '_Repair.pdb'
, '--water=PREDICT'
, '--vdwDesign=1'
, '--output-dir=' + process_dir], cwd=process_dir)
print('Running foldx SequenceDetail')
subprocess.call(['foldx'
, '--command=SequenceDetail'
, '--pdb-dir=' + process_dir
, '--pdb=' + pdbname + '_Repair.pdb'
, '--water=PREDICT'
, '--vdwDesign=1'
, '--output-dir=' + process_dir], cwd=process_dir)
print('\033[95mCOMPLETE: run FoldX (subprocess)\033[0m')
print('\033[95mSTAGE: Print Networks (shell)\033[0m')
for n in range(1,nmuts+1):
print('\033[95mNETWORK:\033[0m', n)
print('\033[96mCommand:\033[0m runPrintNetworks.sh %s %s %s' % (pdbname, str(n), process_dir ))
with suppress(Exception):
subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname, str(n), process_dir])
#print('\033[96mCommand:\033[0m runPrintNetworks.sh %s %s %s' % (pdbname, str(n), process_dir ))
#with suppress(Exception):
#foldx --command=PrintNetworks --pdb="${PDB}_Repair_${n}.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}
print('Running foldx PrintNetworks for mutation', n)
subprocess.call(['foldx'
, '--command=PrintNetworks'
, '--pdb-dir=' + process_dir
, '--pdb=' + pdbname + '_Repair_' + str(n) + '.pdb'
, '--water=PREDICT'
, '--vdwDesign=1'
, '--output-dir=' + process_dir], cwd=process_dir)
#subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname, str(n), process_dir])
print('\033[95mCOMPLETE: Print Networks (shell)\033[0m')
print('\033[95mSTAGE: Rename Mutation Files (shell)\033[0m')
for n in range(1,nmuts+1):
print('\033[95mMUTATION:\033[0m', n)
print('\033[96mCommand:\033[0m mutrenamefiles.sh %s %s %s' % (pdbname, str(n), process_dir ))
# FIXME: this is bad design and needs to be done in a pythonic way
with suppress(Exception):
subprocess.check_output(['bash', 'mutrenamefiles.sh', pdbname, str(n), process_dir])
print('\033[95mCOMPLETE: Rename Mutation Files (shell)\033[0m')
print('\033[95mSTAGE: Rename Files (shell)\033[0m')
# FIXME: this is bad design and needs to be done in a pythonic way
out = subprocess.check_output(['bash','renamefiles.sh', pdbname, process_dir])
print('\033[95mCOMPLETE: Rename Files (shell)\033[0m')
if comp=='y':
print('\033[95mSTAGE: Run Complex (shell)\033[0m')
print('\033[95mSTAGE: Running foldx AnalyseComplex (subprocess)\033[0m')
chain1=chainA
chain2=chainB
with suppress(Exception):
#with suppress(Exception):
#subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir])
subprocess(['foldx --command=AnalyseComplex --pdb="%s_Repair.pdb" --analyseComplexChains=%s,%s --water=PREDICT --vdwDesign=1 --output-dir=%s'] % (pdbname, chain1, chain2, process_dir))
subprocess.call(['foldx'
, '--command=AnalyseComplex'
, '--pdb-dir=' + process_dir
, '--pdb=' + pdbname + '_Repair.pdb'
, '--analyseComplexChains=' + chain1 + ',' + chain2
, '--water=PREDICT'
, '--vdwDesign=1'
, '--output-dir=' + process_dir], cwd=process_dir)
# FIXME why would we ever need to do this?!? Cargo-culted from runcomplex.sh
ac_source = process_dir + '/Summary_' + pdbname + '_Repair_AC.fxout'
ac_dest = process_dir + '/Summary_' + pdbname + '_Repair_AC.txt'
shutil.copyfile(ac_source, ac_dest)
for n in range(1,nmuts+1):
print('\033[95mSTAGE: Run Mutation Complex (shell) for mutation:\033[0m', n)
with suppress(Exception):
subprocess.check_output(['bash','mutruncomplex.sh', pdbname, chain1, chain2, str(n), process_dir])
print('\033[95mCOMPLETE: Run Complex (shell)\033[0m')
print('\033[95mSTAGE: Running foldx AnalyseComplex (subprocess) for mutation:\033[0m', n)
#with suppress(Exception):
# subprocess.check_output(['bash','mutruncomplex.sh', pdbname, chain1, chain2, str(n), process_dir])
subprocess.call(['foldx'
, '--command=AnalyseComplex'
, '--pdb-dir=' + process_dir
, '--pdb=' + pdbname + '_Repair_' + str(n) + '.pdb'
, '--analyseComplexChains=' + chain1 + ',' + chain2
, '--water=PREDICT'
, '--vdwDesign=1'
, '--output-dir=' + process_dir], cwd=process_dir)
# FIXME why would we ever need to do this?!? Cargo-culted from runcomplex.sh
ac_mut_source = process_dir + '/Summary_' + pdbname + '_Repair_' + str(n) +'_AC.fxout'
ac_mut_dest = process_dir + '/Summary_' + pdbname + '_Repair)' + str(n) +'_AC.txt'
shutil.copyfile(ac_mut_source, ac_mut_dest)
print('\033[95mCOMPLETE: foldx AnalyseComplex (subprocess) for mutation:\033[0m', n)
interactions = ['Distances','Electro_RR','Electro_MM','Electro_SM','Electro_SS','Disulfide_RR','Disulfide_MM','Disulfide_SM','Disulfide_SS',
'Hbonds_RR','Hbonds_MM','Hbonds_SM','Hbonds_SS','Partcov_RR','Partcov_MM','Partcov_SM','Partcov_SS','VdWClashes_RR','VdWClashes_MM',