From fa25a30dcf556993ef487728c8d99d5a9b0f52d5 Mon Sep 17 00:00:00 2001
From: Tanushree Tunstall <tanu@tunstall.in>
Date: Mon, 8 Feb 2021 15:44:21 +0000
Subject: [PATCH] fixup broken shell scripts

---
 foldx/test2/mutrenamefiles.sh |  4 +++-
 foldx/test2/renamefiles.sh    |  3 +++
 foldx/test2/runFoldx.py       | 23 ++++++++++++++++++-----
 3 files changed, 24 insertions(+), 6 deletions(-)

diff --git a/foldx/test2/mutrenamefiles.sh b/foldx/test2/mutrenamefiles.sh
index b1d8742..d9f938c 100755
--- a/foldx/test2/mutrenamefiles.sh
+++ b/foldx/test2/mutrenamefiles.sh
@@ -1,6 +1,8 @@
 PDB=$1
 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_${n}_PN.txt
 sed -n '5,190p' Matrix_Hbonds_${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
diff --git a/foldx/test2/renamefiles.sh b/foldx/test2/renamefiles.sh
index e5d8fe9..2a2b193 100755
--- a/foldx/test2/renamefiles.sh
+++ b/foldx/test2/renamefiles.sh
@@ -1,4 +1,7 @@
 PDB=$1
+OUTDIR=$2
+cd ${OUTDIR}
+
 #cd /home/git/LSHTM_analysis/foldx/test
 cp Dif_${PDB}_Repair.fxout Dif_${PDB}_Repair.txt
 sed -i '1,8d' Dif_${PDB}_Repair.txt
diff --git a/foldx/test2/runFoldx.py b/foldx/test2/runFoldx.py
index bf2a835..42db217 100755
--- a/foldx/test2/runFoldx.py
+++ b/foldx/test2/runFoldx.py
@@ -207,31 +207,44 @@ def main():
     print(mutlist)
     print('start')
     #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])
-    
-    print('end')
+    print('\033[95mCOMPLETE: repair PDB\033[0m')
+    print('\033[95mSTAGE: run FoldX (shell)\033[0m')
     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):
-        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):
             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(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):
             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])
+    print('\033[95mCOMPLETE: Rename Files (shell)\033[0m')
 
     if comp=='y':
+        print('\033[95mSTAGE: Run Complex (shell)\033[0m')
         chain1=chainA
         chain2=chainB
         with suppress(Exception):
             subprocess.check_output(['bash','runcomplex.sh', pdbname, chain1, chain2, process_dir])
         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')
 
     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',