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

foldx/runFoldx.py

@@ -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'