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fixup broken shell scripts

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This commit is contained in:
Tanushree Tunstall 2021-02-08 15:44:21 +00:00
parent a67156bc87
commit c9698d7550
3 changed files with 24 additions and 6 deletions
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4
foldx/test2/mutrenamefiles.sh
View file

@ -1,6 +1,8 @@
PDB=$1 PDB=$1
n=$2 n=$2
#cd /home/git/LSHTM_analysis/foldx/test/ OUTDIR=$3
cd ${OUTDIR}
cp Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout Matrix_Hbonds_${PDB}_Repair_${n}_PN.txt cp Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout Matrix_Hbonds_${PDB}_Repair_${n}_PN.txt
sed -n '5,190p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_RR_${PDB}_Repair_${n}_PN.txt sed -n '5,190p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_RR_${PDB}_Repair_${n}_PN.txt
sed -n '194,379p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_MM_${PDB}_Repair_${n}_PN.txt sed -n '194,379p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_MM_${PDB}_Repair_${n}_PN.txt

3
foldx/test2/renamefiles.sh
View file

@ -1,4 +1,7 @@
PDB=$1 PDB=$1
OUTDIR=$2
cd ${OUTDIR}
#cd /home/git/LSHTM_analysis/foldx/test #cd /home/git/LSHTM_analysis/foldx/test
cp Dif_${PDB}_Repair.fxout Dif_${PDB}_Repair.txt cp Dif_${PDB}_Repair.fxout Dif_${PDB}_Repair.txt
sed -i '1,8d' Dif_${PDB}_Repair.txt sed -i '1,8d' Dif_${PDB}_Repair.txt

23
foldx/test2/runFoldx.py
View file

@ -207,31 +207,44 @@ def main():
print(mutlist) print(mutlist)
print('start') print('start')
#subprocess.check_output(['bash','repairPDB.sh', pdbname, process_dir]) #subprocess.check_output(['bash','repairPDB.sh', pdbname, process_dir])
print('\033[95mSTAGE: repair PDB\033[0m')
subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir]) subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
print('\033[95mCOMPLETE: repair PDB\033[0m')
print('end') print('\033[95mSTAGE: run FoldX (shell)\033[0m')
output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir]) output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir])
print('\033[95mCOMPLETE: run FoldX (shell)\033[0m')
print('\033[95mSTAGE: Print Networks (shell)\033[0m')
for n in range(1,nmuts+1): for n in range(1,nmuts+1):
print(n) print('\033[95mNETWORK:\033[0m', n)
print('\033[96mCommand:\033[0m runPrintNetworks.sh %s %s %s' % (pdbname, str(n), process_dir ))
with suppress(Exception): with suppress(Exception):
subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname, str(n), 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): for n in range(1,nmuts+1):
print(n) print('\033[95mMUTATION:\033[0m', n)
print('\033[96mCommand:\033[0m mutrenamefiles.sh %s %s %s' % (pdbname, str(n), process_dir ))
with suppress(Exception): with suppress(Exception):
subprocess.check_output(['bash', 'mutrenamefiles.sh', pdbname, str(n), process_dir]) 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')
out = subprocess.check_output(['bash','renamefiles.sh', pdbname, process_dir]) out = subprocess.check_output(['bash','renamefiles.sh', pdbname, process_dir])
print('\033[95mCOMPLETE: Rename Files (shell)\033[0m')
if comp=='y': if comp=='y':
print('\033[95mSTAGE: Run Complex (shell)\033[0m')
chain1=chainA chain1=chainA
chain2=chainB chain2=chainB
with suppress(Exception): with suppress(Exception):
subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir]) subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir])
for n in range(1,nmuts+1): for n in range(1,nmuts+1):
print('\033[95mSTAGE: Run Mutation Complex (shell) for mutation:\033[0m', n)
with suppress(Exception): with suppress(Exception):
subprocess.check_output(['bash','mutruncomplex.sh', pdbname, chain1, chain2, str(n), process_dir]) subprocess.check_output(['bash','mutruncomplex.sh', pdbname, chain1, chain2, str(n), process_dir])
print('\033[95mCOMPLETE: Run Complex (shell)\033[0m')
interactions = ['Distances','Electro_RR','Electro_MM','Electro_SM','Electro_SS','Disulfide_RR','Disulfide_MM','Disulfide_SM','Disulfide_SS', 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', 'Hbonds_RR','Hbonds_MM','Hbonds_SM','Hbonds_SS','Partcov_RR','Partcov_MM','Partcov_SM','Partcov_SS','VdWClashes_RR','VdWClashes_MM',