fix runFoldx so that it looks for a missing rotabase.txt in the process_dir and also print the foldx command that will be run
This commit is contained in:
parent
d443ecea6b
commit
93a91518e1
1 changed files with 52 additions and 18 deletions
|
|
@ -41,7 +41,7 @@ arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By
|
|||
arg_parser.add_argument('-p', '--process_dir', help = 'Temp processing dir for running foldX. By default, it assmes homedir + <drug> + processing. Make sure it is somewhere with LOTS of storage as it writes all output!') #FIXME
|
||||
|
||||
arg_parser.add_argument('-P', '--pdb_file', help = 'PDB File to process. By default, it assmumes a file called <gene>_complex.pdb in input_dir')
|
||||
arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called <gene>_mcsm_snps.csv exists')
|
||||
arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called <gene>_mcsm_formatted_snps.csv exists')
|
||||
|
||||
# FIXME: Doesn't work with 2 chains yet!
|
||||
arg_parser.add_argument('-c1', '--chain1', help = 'Chain1 ID', default = 'A') # case sensitive
|
||||
|
|
@ -148,6 +148,16 @@ print('Arguments being passed:'
|
|||
, '\noutput file:', outfile_foldx
|
||||
, '\n=============================================================')
|
||||
|
||||
|
||||
# make sure rotabase.txt exists in the process_dir
|
||||
rotabase_file = process_dir + '/' + 'rotabase.txt'
|
||||
|
||||
if Path(rotabase_file).is_file():
|
||||
print(f'rotabase file: {rotabase_file} exists')
|
||||
else:
|
||||
print(f'ERROR: rotabase file: {rotabase_file} does not exist. Please download it and put it in {process_dir}')
|
||||
sys.exit()
|
||||
|
||||
#### Delay for 10 seconds to check the params ####
|
||||
print('Sleeping for 10 seconds to give you time to cancel')
|
||||
time.sleep(10)
|
||||
|
|
@ -235,6 +245,13 @@ def main():
|
|||
nmuts = len(mutlist)
|
||||
print(nmuts)
|
||||
print(mutlist)
|
||||
print('start')
|
||||
#subprocess.check_output(['bash','repairPDB.sh', pdbname, process_dir])
|
||||
print('\033[95mSTAGE: repair PDB\033[0m')
|
||||
print('EXECUTING: repairPDB.sh %s %s %s' % (indir, actual_pdb_filename, process_dir))
|
||||
#subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
|
||||
# once you decide to use the function
|
||||
# repairPDB(pdbname)
|
||||
|
||||
print('start')
|
||||
# some common parameters for foldX
|
||||
|
|
@ -242,61 +259,74 @@ def main():
|
|||
|
||||
print('\033[95mSTAGE: repair PDB (foldx subprocess) \033[0m')
|
||||
print('Running foldx RepairPDB for WT')
|
||||
subprocess.call(['foldx'
|
||||
|
||||
fold_RepairDB = ['foldx'
|
||||
, '--command=RepairPDB'
|
||||
, foldx_common
|
||||
, '--pdb-dir=' + os.path.dirname(pdb_filename)
|
||||
# , '--pdb-dir=' + os.path.dirname(pdb_filename)
|
||||
, '--pdb-dir=' + indir
|
||||
, '--pdb=' + actual_pdb_filename
|
||||
, 'outPDB=true'
|
||||
, '--output-dir=' + process_dir])
|
||||
, '--output-dir=' + process_dir]
|
||||
print('CMD:', fold_RepairDB)
|
||||
subprocess.call(fold_RepairDB)
|
||||
print('\033[95mCOMPLETED STAGE: repair PDB\033[0m')
|
||||
print('\n==========================================================')
|
||||
|
||||
|
||||
print('\033[95mSTAGE: Foldx commands BM, PN and SD (foldx subprocess) for WT\033[0m')
|
||||
print('Running foldx BuildModel for WT')
|
||||
subprocess.call(['foldx'
|
||||
|
||||
foldx_BuildModel = ['foldx'
|
||||
, '--command=BuildModel'
|
||||
, foldx_common
|
||||
, '--pdb-dir=' + process_dir
|
||||
, '--pdb=' + pdbname + '_Repair.pdb'
|
||||
, '--mutant-file="individual_list_' + pdbname +'.txt"'
|
||||
, '--mutant-file=' + process_dir + '/' + 'individual_list_' + pdbname +'.txt'
|
||||
, 'outPDB=true'
|
||||
, '--numberOfRuns=1'
|
||||
, '--output-dir=' + process_dir], cwd=process_dir)
|
||||
, '--output-dir=' + process_dir]
|
||||
print('CMD:', foldx_BuildModel)
|
||||
subprocess.call( foldx_BuildModel, cwd=process_dir)
|
||||
|
||||
print('Running foldx PrintNetworks for WT')
|
||||
subprocess.call(['foldx'
|
||||
foldx_PrintNetworks = ['foldx'
|
||||
, '--command=PrintNetworks'
|
||||
, '--pdb-dir=' + process_dir
|
||||
, '--pdb=' + pdbname + '_Repair.pdb'
|
||||
, '--water=PREDICT'
|
||||
, '--vdwDesign=1'
|
||||
, '--output-dir=' + process_dir], cwd=process_dir)
|
||||
, '--output-dir=' + process_dir]
|
||||
print('CMD:', foldx_PrintNetworks)
|
||||
subprocess.call(foldx_PrintNetworks, cwd=process_dir)
|
||||
|
||||
print('Running foldx SequenceDetail for WT')
|
||||
subprocess.call(['foldx'
|
||||
foldx_SequenceDetail = ['foldx'
|
||||
, '--command=SequenceDetail'
|
||||
, '--pdb-dir=' + process_dir
|
||||
, '--pdb=' + pdbname + '_Repair.pdb'
|
||||
, '--water=PREDICT'
|
||||
, '--vdwDesign=1'
|
||||
, '--output-dir=' + process_dir], cwd=process_dir)
|
||||
, '--output-dir=' + process_dir]
|
||||
print('CMD:', foldx_SequenceDetail)
|
||||
subprocess.call(foldx_SequenceDetail , cwd=process_dir)
|
||||
|
||||
print('\033[95mCOMPLETED STAGE: Foldx commands BM, PN and SD\033[0m')
|
||||
print('\n==========================================================')
|
||||
|
||||
|
||||
print('\033[95mSTAGE: Print Networks (foldx subprocess) for MT\033[0m')
|
||||
for n in range(1,nmuts+1):
|
||||
print('\033[95mNETWORK:\033[0m', n)
|
||||
print('Running foldx PrintNetworks for mutation', n)
|
||||
subprocess.call(['foldx'
|
||||
foldx_PrintNetworksMT = ['foldx'
|
||||
, '--command=PrintNetworks'
|
||||
, '--pdb-dir=' + process_dir
|
||||
, '--pdb=' + pdbname + '_Repair_' + str(n) + '.pdb'
|
||||
, '--water=PREDICT'
|
||||
, '--vdwDesign=1'
|
||||
, '--output-dir=' + process_dir], cwd=process_dir)
|
||||
, '--output-dir=' + process_dir]
|
||||
print('CMD:', foldx_PrintNetworksMT)
|
||||
subprocess.call( foldx_PrintNetworksMT , cwd=process_dir)
|
||||
print('\033[95mCOMPLETED STAGE: Print Networks (foldx subprocess) for MT\033[0m')
|
||||
print('\n==========================================================')
|
||||
|
||||
|
|
@ -323,14 +353,16 @@ def main():
|
|||
print('\033[95mSTAGE: Running foldx AnalyseComplex (foldx subprocess) for WT\033[0m')
|
||||
chain1=chainA
|
||||
chain2=chainB
|
||||
subprocess.call(['foldx'
|
||||
foldx_AnalyseComplex = ['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)
|
||||
, '--output-dir=' + process_dir]
|
||||
print('CMD:',foldx_AnalyseComplex)
|
||||
subprocess.call(foldx_AnalyseComplex, 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'
|
||||
|
|
@ -340,14 +372,16 @@ def main():
|
|||
|
||||
for n in range(1,nmuts+1):
|
||||
print('\033[95mSTAGE: Running foldx AnalyseComplex (foldx subprocess) for mutation:\033[0m', n)
|
||||
subprocess.call(['foldx'
|
||||
foldx_AnalyseComplex = ['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)
|
||||
, '--output-dir=' + process_dir]
|
||||
print('CMD:', foldx_AnalyseComplex)
|
||||
subprocess.call( foldx_AnalyseComplex , 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'
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue