test2 bugfixes

foldx/runFoldx.py

@@ -35,11 +35,12 @@ arg_parser.add_argument('-g', '--gene',     help = 'gene name (case sensitive)',
 arg_parser.add_argument('--datadir', help = 'Data Directory. By default, it assmumes homedir + git/Data')
 arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
 arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
-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!')
+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('-pdb', '--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')
 
+# FIXME: Doesn't work with 2 chains yet!
 arg_parser.add_argument('-c1', '--chain1',    help = 'Chain1 ID', default = 'A') # case sensitive
 arg_parser.add_argument('-c2', '--chain2',    help = 'Chain2 ID', default = 'B') # case sensitive
 
@@ -101,7 +102,7 @@ actual_pdb_filename = Path(infile_pdb).name
 if mut_filename:
     mutation_file = mut_filename
 else:
-    mutation_file =  gene.lower() + '_mcsm_snps.csv'
+    mutation_file =  gene.lower() + '_mcsm_formatted_snps.csv'
 
 infile_muts = outdir + '/' + mutation_file
 

foldx/runcomplex.sh

@@ -7,4 +7,3 @@ logger "Running runcomplex"
 foldx --command=AnalyseComplex --pdb="${PDB}_Repair.pdb" --analyseComplexChains=${A},${B} --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}
 cp ${OUTDIR}/Summary_${PDB}_Repair_AC.fxout ${OUTDIR}/Summary_${PDB}_Repair_AC.txt
 #sed -i .bak -e 1,8d ${OUTDIR}/Summary_${PDB}_Repair_AC.txt 
-

foldx/test2/mutrenamefiles.sh

@@ -0,0 +1,61 @@
+PDB=$1
+n=$2
+#cd /home/git/LSHTM_analysis/foldx/test/
+cp Matrix_Hbonds_${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_${n}_PN.txt
+sed -n '383,568p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_SM_${PDB}_Repair_${n}_PN.txt
+sed -n '572,757p' Matrix_Hbonds_${PDB}_Repair_${n}_PN.fxout > Matrix_Hbonds_SS_${PDB}_Repair_${n}_PN.txt
+cp Matrix_Distances_${PDB}_Repair_${n}_PN.fxout Matrix_Distances_${PDB}_Repair_${n}_PN.txt
+sed -i '1,4d' Matrix_Distances_${PDB}_Repair_${n}_PN.txt
+cp Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout Matrix_Volumetric_${PDB}_Repair_${n}_PN.txt
+sed -n '5,190p' Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout > Matrix_Volumetric_RR_${PDB}_Repair_${n}_PN.txt
+sed -n '194,379p' Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout > Matrix_Volumetric_MM_${PDB}_Repair_${n}_PN.txt
+sed -n '383,568p' Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout > Matrix_Volumetric_SM_${PDB}_Repair_${n}_PN.txt
+sed -n '572,757p' Matrix_Volumetric_${PDB}_Repair_${n}_PN.fxout > Matrix_Volumetric_SS_${PDB}_Repair_${n}_PN.txt
+cp Matrix_Electro_${PDB}_Repair_${n}_PN.fxout Matrix_Electro_${PDB}_Repair_${n}_PN.txt
+sed -n '5,190p' Matrix_Electro_${PDB}_Repair_${n}_PN.fxout > Matrix_Electro_RR_${PDB}_Repair_${n}_PN.txt
+sed -n '194,379p' Matrix_Electro_${PDB}_Repair_${n}_PN.fxout > Matrix_Electro_MM_${PDB}_Repair_${n}_PN.txt
+sed -n '383,568p' Matrix_Electro_${PDB}_Repair_${n}_PN.fxout > Matrix_Electro_SM_${PDB}_Repair_${n}_PN.txt
+sed -n '572,757p' Matrix_Electro_${PDB}_Repair_${n}_PN.fxout > Matrix_Electro_SS_${PDB}_Repair_${n}_PN.txt
+cp Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout Matrix_Disulfide_${PDB}_Repair_${n}_PN.txt
+sed -n '5,190p' Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout > Matrix_Disulfide_RR_${PDB}_Repair_${n}_PN.txt
+sed -n '194,379p' Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout > Matrix_Disulfide_MM_${PDB}_Repair_${n}_PN.txt
+sed -n '383,568p' Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout > Matrix_Disulfide_SM_${PDB}_Repair_${n}_PN.txt
+sed -n '572,757p' Matrix_Disulfide_${PDB}_Repair_${n}_PN.fxout > Matrix_Disulfide_SS_${PDB}_Repair_${n}_PN.txt
+cp Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout Matrix_Partcov_${PDB}_Repair_${n}_PN.txt
+sed -n '5,190p' Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout > Matrix_Partcov_RR_${PDB}_Repair_${n}_PN.txt
+sed -n '194,379p' Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout > Matrix_Partcov_MM_${PDB}_Repair_${n}_PN.txt
+sed -n '383,568p' Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout > Matrix_Partcov_SM_${PDB}_Repair_${n}_PN.txt
+sed -n '572,757p' Matrix_Partcov_${PDB}_Repair_${n}_PN.fxout > Matrix_Partcov_SS_${PDB}_Repair_${n}_PN.txt
+cp Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout Matrix_VdWClashes_${PDB}_Repair_${n}_PN.txt
+sed -n '5,190p' Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout > Matrix_VdWClashes_RR_${PDB}_Repair_${n}_PN.txt
+sed -n '194,379p' Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout > Matrix_VdWClashes_MM_${PDB}_Repair_${n}_PN.txt
+sed -n '383,568p' Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout > Matrix_VdWClashes_SM_${PDB}_Repair_${n}_PN.txt
+sed -n '572,757p' Matrix_VdWClashes_${PDB}_Repair_${n}_PN.fxout > Matrix_VdWClashes_SS_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_Disulfide_${PDB}_Repair_${n}_PN.fxout AllAtoms_Disulfide_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Disulfide_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_Electro_${PDB}_Repair_${n}_PN.fxout AllAtoms_Electro_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Electro_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.fxout AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_Partcov_${PDB}_Repair_${n}_PN.fxout AllAtoms_Partcov_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Partcov_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.fxout AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.txt
+cp AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.fxout AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.txt
+sed -i '1,2d' AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.fxout InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Distances_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Distances_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Distances_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Electro_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Electro_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Electro_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.txt
+cp InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.txt
+sed -i '1,5d' InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.txt

foldx/test2/mutruncomplex.sh

@@ -0,0 +1,10 @@
+PDB=$1
+A=$2
+B=$3
+n=$4
+OUTDIR=$5
+cd ${OUTDIR}
+logger "Running mutruncomplex"
+foldx --command=AnalyseComplex --pdb="${PDB}_Repair_${n}.pdb" --analyseComplexChains=${A},${B} --water=PREDICT --vdwDesign=1
+cp ${OUTDIR}/Summary_${PDB}_Repair_${n}_AC.fxout ${OUTDIR}/Summary_${PDB}_Repair_${n}_AC.txt
+#sed -i .bak -e 1,8d ${OUTDIR}/Summary_${PDB}_Repair_${n}_AC.txt 

foldx/test2/renamefiles.sh

@@ -0,0 +1,62 @@
+PDB=$1
+#cd /home/git/LSHTM_analysis/foldx/test
+cp Dif_${PDB}_Repair.fxout Dif_${PDB}_Repair.txt
+sed -i '1,8d' Dif_${PDB}_Repair.txt
+cp Matrix_Hbonds_${PDB}_Repair_PN.fxout Matrix_Hbonds_${PDB}_Repair_PN.txt
+sed -n '5,190p' Matrix_Hbonds_${PDB}_Repair_PN.fxout > Matrix_Hbonds_RR_${PDB}_Repair_PN.txt
+sed -n '194,379p' Matrix_Hbonds_${PDB}_Repair_PN.fxout > Matrix_Hbonds_MM_${PDB}_Repair_PN.txt
+sed -n '383,568p' Matrix_Hbonds_${PDB}_Repair_PN.fxout > Matrix_Hbonds_SM_${PDB}_Repair_PN.txt
+sed -n '572,757p' Matrix_Hbonds_${PDB}_Repair_PN.fxout > Matrix_Hbonds_SS_${PDB}_Repair_PN.txt
+cp Matrix_Distances_${PDB}_Repair_PN.fxout Matrix_Distances_${PDB}_Repair_PN.txt
+sed -i '1,4d' Matrix_Distances_${PDB}_Repair_PN.txt
+cp Matrix_Volumetric_${PDB}_Repair_PN.fxout Matrix_Volumetric_${PDB}_Repair_PN.txt
+sed -n '5,190p' Matrix_Volumetric_${PDB}_Repair_PN.fxout > Matrix_Volumetric_RR_${PDB}_Repair_PN.txt
+sed -n '194,379p' Matrix_Volumetric_${PDB}_Repair_PN.fxout > Matrix_Volumetric_MM_${PDB}_Repair_PN.txt
+sed -n '383,568p' Matrix_Volumetric_${PDB}_Repair_PN.fxout > Matrix_Volumetric_SM_${PDB}_Repair_PN.txt
+sed -n '572,757p' Matrix_Volumetric_${PDB}_Repair_PN.fxout > Matrix_Volumetric_SS_${PDB}_Repair_PN.txt
+cp Matrix_Electro_${PDB}_Repair_PN.fxout Matrix_Electro_${PDB}_Repair_PN.txt
+sed -n '5,190p' Matrix_Electro_${PDB}_Repair_PN.fxout > Matrix_Electro_RR_${PDB}_Repair_PN.txt
+sed -n '194,379p' Matrix_Electro_${PDB}_Repair_PN.fxout > Matrix_Electro_MM_${PDB}_Repair_PN.txt
+sed -n '383,568p' Matrix_Electro_${PDB}_Repair_PN.fxout > Matrix_Electro_SM_${PDB}_Repair_PN.txt
+sed -n '572,757p' Matrix_Electro_${PDB}_Repair_PN.fxout > Matrix_Electro_SS_${PDB}_Repair_PN.txt
+cp Matrix_Disulfide_${PDB}_Repair_PN.fxout Matrix_Disulfide_${PDB}_Repair_PN.txt
+sed -n '5,190p' Matrix_Disulfide_${PDB}_Repair_PN.fxout > Matrix_Disulfide_RR_${PDB}_Repair_PN.txt
+sed -n '194,379p' Matrix_Disulfide_${PDB}_Repair_PN.fxout > Matrix_Disulfide_MM_${PDB}_Repair_PN.txt
+sed -n '383,568p' Matrix_Disulfide_${PDB}_Repair_PN.fxout > Matrix_Disulfide_SM_${PDB}_Repair_PN.txt
+sed -n '572,757p' Matrix_Disulfide_${PDB}_Repair_PN.fxout > Matrix_Disulfide_SS_${PDB}_Repair_PN.txt
+cp Matrix_Partcov_${PDB}_Repair_PN.fxout Matrix_Partcov_${PDB}_Repair_PN.txt
+sed -n '5,190p' Matrix_Partcov_${PDB}_Repair_PN.fxout > Matrix_Partcov_RR_${PDB}_Repair_PN.txt
+sed -n '194,379p' Matrix_Partcov_${PDB}_Repair_PN.fxout > Matrix_Partcov_MM_${PDB}_Repair_PN.txt
+sed -n '383,568p' Matrix_Partcov_${PDB}_Repair_PN.fxout > Matrix_Partcov_SM_${PDB}_Repair_PN.txt
+sed -n '572,757p' Matrix_Partcov_${PDB}_Repair_PN.fxout > Matrix_Partcov_SS_${PDB}_Repair_PN.txt
+cp Matrix_VdWClashes_${PDB}_Repair_PN.fxout Matrix_VdWClashes_${PDB}_Repair_PN.txt
+sed -n '5,190p' Matrix_VdWClashes_${PDB}_Repair_PN.fxout > Matrix_VdWClashes_RR_${PDB}_Repair_PN.txt
+sed -n '194,379p' Matrix_VdWClashes_${PDB}_Repair_PN.fxout > Matrix_VdWClashes_MM_${PDB}_Repair_PN.txt
+sed -n '383,568p' Matrix_VdWClashes_${PDB}_Repair_PN.fxout > Matrix_VdWClashes_SM_${PDB}_Repair_PN.txt
+sed -n '572,757p' Matrix_VdWClashes_${PDB}_Repair_PN.fxout > Matrix_VdWClashes_SS_${PDB}_Repair_PN.txt
+cp AllAtoms_Disulfide_${PDB}_Repair_PN.fxout AllAtoms_Disulfide_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Disulfide_${PDB}_Repair_PN.txt
+cp AllAtoms_Electro_${PDB}_Repair_PN.fxout AllAtoms_Electro_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Electro_${PDB}_Repair_PN.txt
+cp AllAtoms_Hbonds_${PDB}_Repair_PN.fxout AllAtoms_Hbonds_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Hbonds_${PDB}_Repair_PN.txt
+cp AllAtoms_Partcov_${PDB}_Repair_PN.fxout AllAtoms_Partcov_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Partcov_${PDB}_Repair_PN.txt
+cp AllAtoms_VdWClashes_${PDB}_Repair_PN.fxout AllAtoms_VdWClashes_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_VdWClashes_${PDB}_Repair_PN.txt
+cp AllAtoms_Volumetric_${PDB}_Repair_PN.fxout AllAtoms_Volumetric_${PDB}_Repair_PN.txt
+sed -i '1,2d' AllAtoms_Volumetric_${PDB}_Repair_PN.txt
+cp InteractingResidues_VdWClashes_${PDB}_Repair_PN.fxout InteractingResidues_VdWClashes_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_VdWClashes_${PDB}_Repair_PN.txt
+cp InteractingResidues_Distances_${PDB}_Repair_PN.fxout InteractingResidues_Distances_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Distances_${PDB}_Repair_PN.txt
+cp InteractingResidues_Electro_${PDB}_Repair_PN.fxout InteractingResidues_Electro_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Electro_${PDB}_Repair_PN.txt
+cp InteractingResidues_Hbonds_${PDB}_Repair_PN.fxout InteractingResidues_Hbonds_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Hbonds_${PDB}_Repair_PN.txt
+cp InteractingResidues_Partcov_${PDB}_Repair_PN.fxout InteractingResidues_Partcov_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Partcov_${PDB}_Repair_PN.txt
+cp InteractingResidues_Volumetric_${PDB}_Repair_PN.fxout InteractingResidues_Volumetric_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Volumetric_${PDB}_Repair_PN.txt
+cp InteractingResidues_Disulfide_${PDB}_Repair_PN.fxout InteractingResidues_Disulfide_${PDB}_Repair_PN.txt
+sed -i '1,5d' InteractingResidues_Disulfide_${PDB}_Repair_PN.txt

foldx/test2/repairPDB.sh

@@ -0,0 +1,9 @@
+INDIR=$1
+PDB=$2
+OUTDIR=$3
+
+logger "Running repairPDB"
+
+#foldx --command=RepairPDB --pdb="${PDB}.pdb" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 outPDB=true --output-dir=${OUTDIR}
+
+foldx --command=RepairPDB --pdb-dir=${INDIR} --pdb=${PDB} --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 outPDB=true --output-dir=${OUTDIR}

foldx/test2/runFoldx.py

@@ -0,0 +1,344 @@
+#!/usr/bin/env python3
+import subprocess
+import os
+import sys
+import numpy as np
+import pandas as pd
+from contextlib import suppress
+from pathlib import Path
+import re
+import csv
+import argparse
+#https://realpython.com/python-pathlib/
+
+# FIXME
+#strong dependency of file and path names
+#cannot pass file with path. Need to pass them separately
+#assumptions made for dir struc as standard
+#datadir + drug + input
+
+#=======================================================================
+#%% specify input and curr dir
+homedir = os.path.expanduser('~')
+
+# set working dir
+os.getcwd()
+#os.chdir(homedir + '/git/LSHTM_analysis/foldx/')
+#os.getcwd()
+
+#=======================================================================
+#%% command line args
+arg_parser = argparse.ArgumentParser()
+
+arg_parser.add_argument('-d', '--drug',     help = 'drug name', default = None)
+arg_parser.add_argument('-g', '--gene',     help = 'gene name (case sensitive)', default = None)
+
+arg_parser.add_argument('--datadir', help = 'Data Directory. By default, it assmumes homedir + git/Data')
+arg_parser.add_argument('-i', '--input_dir', help = 'Input dir containing pdb files. By default, it assmumes homedir + <drug> + input')
+arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + <drug> + output')
+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('-pdb', '--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')
+
+# FIXME: Doesn't work with 2 chains yet!
+arg_parser.add_argument('-c1', '--chain1',    help = 'Chain1 ID', default = 'A') # case sensitive
+arg_parser.add_argument('-c2', '--chain2',    help = 'Chain2 ID', default = 'B') # case sensitive
+
+args = arg_parser.parse_args()
+#=======================================================================
+#%% variable assignment: input and output 
+#drug = 'pyrazinamide'
+#gene = 'pncA'
+#gene_match = gene + '_p.'
+#%%=====================================================================
+# Command line options
+drug         = args.drug
+gene         = args.gene
+
+datadir      = args.datadir
+indir        = args.input_dir
+outdir       = args.output_dir
+process_dir  = args.process_dir
+
+mut_filename = args.mutation_file
+chainA       = args.chain1
+chainB       = args.chain2
+pdb_filename = args.pdb_file
+
+# os.path.splitext will fail interestingly with file.pdb.txt.zip
+#pdb_name = os.path.splitext(pdb_file)[0]
+# Just the filename, thanks
+#pdb_name = Path(in_filename_pdb).stem
+
+#==============
+# directories
+#==============
+if not datadir:
+    datadir = homedir + '/' + 'git/Data'
+    
+if not indir:
+    indir = datadir + '/' + drug + '/input'
+    
+if not outdir:
+    outdir = datadir + '/' + drug + '/output'
+
+#TODO: perhaps better handled by refactoring code to prevent generating lots of output files!
+#if not process_dir:
+#    process_dir = datadir + '/' + drug + '/processing'
+
+# Make all paths absolute in case the user forgot
+indir = os.path.abspath(indir)
+process_dir = os.path.abspath(process_dir)
+outdir = os.path.abspath(outdir)
+datadir = os.path.abspath(datadir)
+
+#=======
+# input
+#=======
+# FIXME
+if pdb_filename:
+    pdb_name = Path(pdb_filename).stem
+else:
+    pdb_filename = gene.lower() + '_complex.pdb'
+    pdb_name = Path(pdb_filename).stem
+
+infile_pdb = indir + '/' + pdb_filename
+actual_pdb_filename = Path(infile_pdb).name
+
+if mut_filename:
+    mutation_file = os.path.abspath(mut_filename)
+    infile_muts = mutation_file
+    print('User-provided mutation file in use:', infile_muts)
+else:
+    mutation_file =  gene.lower() + '_mcsm_formatted_snps.csv'
+    infile_muts = outdir + '/' + mutation_file
+    print('WARNING: Assuming default mutation file:', infile_muts)
+
+#=======
+# output 
+#=======
+out_filename = gene.lower() + '_foldx.csv'
+outfile_foldx =  outdir + '/' + out_filename
+
+print('Arguments being passed:'
+, '\nDrug:', args.drug
+, '\ngene:', args.gene
+, '\ninput dir:', indir
+, '\nprocess dir:', process_dir
+, '\noutput dir:', outdir
+, '\npdb file:', infile_pdb
+, '\npdb name:', pdb_name
+, '\nactual pdb name:', actual_pdb_filename
+, '\nmutation file:', infile_muts
+, '\nchain1:', args.chain1
+, '\noutput file:', outfile_foldx
+, '\n=============================================================')
+#=======================================================================
+
+def getInteractionEnergy(filename):
+    data = pd.read_csv(filename,sep = '\t')
+    return data['Interaction Energy'].loc[0]
+
+def getInteractions(filename):
+    data = pd.read_csv(filename, index_col = 0, header = 0, sep = '\t')
+    contactList = getIndexes(data,1)
+    number = len(contactList)
+    return number
+
+def formatMuts(mut_file,pdbname):
+    with open(mut_file) as csvfile:
+        readCSV = csv.reader(csvfile)
+        muts = []
+        for row in readCSV:
+                mut = row[0]
+                muts.append(mut)
+        
+    mut_list = []
+    outfile = process_dir + '/individual_list_' + pdbname + '.txt'
+    with open(outfile, 'w') as output:
+        for m in muts:
+                print(m)
+                mut = m[:1] + chainA+ m[1:] 
+                mut_list.append(mut)
+                mut = mut + ';'
+                print(mut)
+                output.write(mut)
+                output.write('\n')
+    return mut_list
+
+def getIndexes(data, value):
+    colnames = data.columns.values
+    listOfPos = list()
+    result = data.isin([value])
+    result.columns = colnames
+    seriesdata = result.any()
+    columnNames = list(seriesdata[seriesdata==True].index)
+    for col in columnNames:
+        rows = list(result[col][result[col]==True].index)
+        
+        for row in rows:
+            listOfPos.append((row,col))
+    
+    return listOfPos
+
+def loadFiles(df):
+    # load a text file in to np matrix
+    resultList = []
+    f = open(df,'r')
+    for line in f:
+        line = line.rstrip('\n')
+        aVals = line.split('\t')
+        fVals = list(map(np.float32, sVals))
+        resultList.append(fVals)
+    f.close()
+    return np.asarray(resultList, dtype=np.float32)
+
+#=======================================================================    
+def main():
+    pdbname = pdb_name
+    comp = '' # for complex only
+    mut_filename = infile_muts #pnca_mcsm_snps.csv
+    mutlist = formatMuts(mut_filename, pdbname)
+
+    print(mutlist)
+    nmuts = len(mutlist)
+    print(nmuts)
+    print(mutlist)
+    print('start')
+    #subprocess.check_output(['bash','repairPDB.sh', pdbname, process_dir])
+    subprocess.check_output(['bash','repairPDB.sh', indir, actual_pdb_filename, process_dir])
+    
+    print('end')
+    output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname, process_dir])
+    
+    for n in range(1,nmuts+1):
+        print(n)
+        with suppress(Exception):
+            subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname, str(n), process_dir])
+        
+    for n in range(1,nmuts+1):
+        print(n)
+        with suppress(Exception):
+            subprocess.check_output(['bash', 'mutrenamefiles.sh', pdbname, str(n), process_dir])
+            
+    out = subprocess.check_output(['bash','renamefiles.sh', pdbname, process_dir])
+
+    if comp=='y':
+        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):
+            with suppress(Exception):
+                subprocess.check_output(['bash','mutruncomplex.sh', pdbname, chain1, chain2, str(n), process_dir])
+
+    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',
+                    'VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS']
+    
+    dGdatafile = process_dir + '/Dif_' + pdbname + '_Repair.txt'
+    dGdata = pd.read_csv(dGdatafile, sep = '\t')
+    
+    ddG=[]
+    print('ddG')
+    print(len(dGdata))
+    for i in range(0,len(dGdata)):
+        ddG.append(dGdata['total energy'].loc[i])
+    
+
+    nint = len(interactions)
+    wt_int = []
+
+    for i in interactions:
+        filename = process_dir + '/Matrix_' + i + '_'+ pdbname + '_Repair_PN.txt'
+        wt_int.append(getInteractions(filename))
+    print('wt')
+    print(wt_int)
+    
+    ntotal = nint+1
+    print(ntotal)
+    print(nmuts)
+    data = np.empty((ntotal,nmuts))
+    data[0] = ddG
+    print(data)
+    for i in range(0,len(interactions)):
+        d=[]
+        p=0
+        for n in range(1, nmuts+1):
+            print(i)
+            filename = process_dir + '/Matrix_' + interactions[i] + '_' + pdbname + '_Repair_' + str(n) + '_PN.txt'
+            mut = getInteractions(filename)
+            diff = wt_int[i] - mut
+            print(diff)
+            print(wt_int[i])
+            print(mut)
+            d.append(diff)
+        print(d)
+        data[i+1] = d    
+        
+    interactions = ['ddG', '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','VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS']   
+
+    print(interactions)
+
+    IE = []
+    if comp=='y':
+        wtfilename = process_dir + '/Summary_' + pdbname + '_Repair_AC.txt'
+        wtE = getInteractionEnergy(wtfilename)
+        print(wtE)
+        for n in range(1,nmuts+1):
+            print(n)
+            filename = process_dir + '/Summary_' + pdbname + '_Repair_' + str(n) + '_AC.txt'
+            mutE = getInteractionEnergy(filename)
+            print(mutE)
+            diff = wtE - mutE
+            print(diff)
+            IE.append(diff)
+        print(IE)
+        IEresults = pd.DataFrame(IE,columns = ['Interaction Energy'], index = mutlist)
+        IEfilename = 'foldx_complexresults_'+pdbname+'.csv'
+        IEresults.to_csv(IEfilename)
+        print(len(IE))
+        data = np.append(data,[IE], axis = 0)
+        print(data)
+        interactions = ['ddG','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','VdWClashes_SM','VdWClashes_SS','Volumetric_RR','Volumetric_MM','Volumetric_SM','Volumetric_SS','Interaction Energy']  
+
+    mut_file = process_dir + '/individual_list_' + pdbname + '.txt'
+    with open(mut_file) as csvfile:
+        readCSV = csv.reader(csvfile)
+        mutlist = []
+        for row in readCSV:
+                mut = row[0]
+                mutlist.append(mut)
+    print(mutlist)
+    print(len(mutlist))
+    print(data)
+    results = pd.DataFrame(data, columns = mutlist, index = interactions)
+    results.append(ddG)
+    #print(results.head())
+    
+    # my style formatted results
+    results2 = results.T # transpose df
+    results2.index.name = 'mutationinformation' # assign name to index
+    results2 = results2.reset_index() # turn it into a columns
+  
+    results2['mutationinformation'] = results2['mutationinformation'].replace({r'([A-Z]{1})[A-Z]{1}([0-9]+[A-Z]{1});' : r'\1 \2'}, regex = True) # capture mcsm style muts (i.e not the chain id)
+    results2['mutationinformation'] = results2['mutationinformation'].str.replace(' ', '') # remove empty space
+    
+    results2.rename(columns = {'Distances': 'Contacts'}, inplace = True)
+        
+    # lower case columns
+    results2.columns = results2.columns.str.lower()
+    
+    print('Writing file in the format below:\n'
+        , results2.head()
+        , '\nNo. of rows:', len(results2)
+        , '\nNo. of cols:', len(results2.columns))
+    
+    outputfilename = outfile_foldx   
+    #outputfilename = 'foldx_results_' + pdbname + '.csv'
+    #results.to_csv(outputfilename)
+    results2.to_csv(outputfilename, index = False)
+    
+if __name__ == '__main__':
+    main()

foldx/test2/runFoldx_test.py

@@ -0,0 +1,250 @@
+#!/usr/bin/env python3
+import subprocess
+import os
+import numpy as np
+import pandas as pd
+from contextlib import suppress
+import re
+import csv
+
+def getInteractions(filename):
+    data = pd.read_csv(filename, index_col=0, header =0, sep="\t")
+    contactList = getIndexes(data,1)
+    print(contactList)
+    number = len(contactList)
+    return number
+
+def formatMuts(mut_file,pdbname):  
+    with open(mut_file) as csvfile:
+        readCSV = csv.reader(csvfile)
+        muts = []
+        for row in readCSV:
+                mut = row[0]
+                muts.append(mut)
+        
+    mut_list = []
+    outfile = "/home/tanu/git/LSHTM_analysis/foldx/test2/individual_list_"+pdbname+".txt"
+    with open(outfile, "w") as output:
+        for m in muts:
+                print(m)
+                mut = m[:1]+'A'+m[1:]
+                mut_list.append(mut)
+                mut = mut + ";"
+                print(mut)
+                output.write(mut)
+                output.write("\n")
+    return mut_list
+
+def getIndexes(data, value):
+    colnames = data.columns.values
+    listOfPos = list()
+    result = data.isin([value])
+    result.columns=colnames
+    seriesdata = result.any()
+    columnNames = list(seriesdata[seriesdata==True].index)
+    for col in columnNames:
+        rows = list(result[col][result[col]==True].index)
+        
+        for row in rows:
+            listOfPos.append((row,col))
+    
+    return listOfPos
+
+def loadFiles(df):
+    # load a text file in to np matrix
+    resultList = []
+    f = open(df,'r')
+    for line in f:
+        line = line.rstrip('\n')
+        aVals = line.split("\t")
+        fVals = list(map(np.float32, sVals))
+        resultList.append(fVals)
+    f.close()
+    return np.asarray(resultList, dtype=np.float32)
+    
+#=======================================================================
+def main():
+    pdbname = '3pl1'
+    mut_filename = "pnca_muts_sample.csv"
+    mutlist = formatMuts(mut_filename, pdbname)
+
+    print(mutlist)
+    nmuts = len(mutlist)+1
+    print(nmuts)
+    print(mutlist)
+    print("start")
+
+    output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname])
+    print("end")
+    for n in range(1,nmuts):
+        print(n)
+        with suppress(Exception):
+            subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname,str(n)])
+        
+    for n in range(1,nmuts):
+        print(n)
+        with suppress(Exception):
+            subprocess.check_output(['bash', 'mutrenamefiles.sh', pdbname,str(n)])
+
+            
+    out = subprocess.check_output(['bash','renamefiles.sh',pdbname])
+    
+    dGdatafile = "/home/tanu/git/LSHTM_analysis/foldx/test2/Dif_"+pdbname+"_Repair.txt"
+    dGdata = pd.read_csv(dGdatafile, sep="\t")
+    print(dGdata)
+    ddG=[]
+    for i in range(0,len(dGdata)):
+        ddG.append(dGdata['total energy'].loc[i])
+    print(ddG)
+    distfile = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Distances_"+pdbname+"_Repair_PN.txt"
+    wt_nc = getInteractions(distfile)
+    
+    elecfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_RR_"+pdbname+"_Repair_PN.txt"
+    wt_neRR = getInteractions(elecfileRR)
+
+    elecfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_MM_"+pdbname+"_Repair_PN.txt"
+    wt_neMM = getInteractions(elecfileMM)
+    
+    elecfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_SM_"+pdbname+"_Repair_PN.txt"
+    wt_neSM = getInteractions(elecfileSM)
+
+    elecfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_SS_"+pdbname+"_Repair_PN.txt"
+    wt_neSS = getInteractions(elecfileSS)
+
+    disufileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_RR_"+pdbname+"_Repair_PN.txt"
+    wt_ndRR = getInteractions(disufileRR)
+
+    disufileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_MM_"+pdbname+"_Repair_PN.txt"
+    wt_ndMM = getInteractions(disufileMM)
+
+    disufileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_SM_"+pdbname+"_Repair_PN.txt"
+    wt_ndSM = getInteractions(disufileSM)
+
+    disufileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_SS_"+pdbname+"_Repair_PN.txt"
+    wt_ndSS = getInteractions(disufileSS)
+
+    hbndfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_RR_"+pdbname+"_Repair_PN.txt"
+    wt_nhRR = getInteractions(hbndfileRR)
+
+    hbndfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_MM_"+pdbname+"_Repair_PN.txt"
+    wt_nhMM = getInteractions(hbndfileMM)
+
+    hbndfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_SM_"+pdbname+"_Repair_PN.txt"
+    wt_nhSM = getInteractions(hbndfileSM)
+
+    hbndfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_SS_"+pdbname+"_Repair_PN.txt"
+    wt_nhSS = getInteractions(hbndfileSS)
+
+    partfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_RR_"+pdbname+"_Repair_PN.txt"
+    wt_npRR = getInteractions(partfileRR)
+
+    partfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_MM_"+pdbname+"_Repair_PN.txt"
+    wt_npMM = getInteractions(partfileMM)
+
+    partfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_SM_"+pdbname+"_Repair_PN.txt"
+    wt_npSM = getInteractions(partfileSM)
+
+    partfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_SS_"+pdbname+"_Repair_PN.txt"
+    wt_npSS = getInteractions(partfileSS)
+
+    vdwcfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_RR_"+pdbname+"_Repair_PN.txt"
+    wt_nvRR = getInteractions(vdwcfileRR)
+  
+    vdwcfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_MM_"+pdbname+"_Repair_PN.txt"
+    wt_nvMM = getInteractions(vdwcfileMM)
+
+    vdwcfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_SM_"+pdbname+"_Repair_PN.txt"
+    wt_nvSM = getInteractions(vdwcfileSM)
+
+    vdwcfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_SS_"+pdbname+"_Repair_PN.txt"
+    wt_nvSS = getInteractions(vdwcfileSS)
+
+    volufileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_RR_"+pdbname+"_Repair_PN.txt"
+    wt_nvoRR = getInteractions(volufileRR)
+
+    volufileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_MM_"+pdbname+"_Repair_PN.txt"
+    wt_nvoMM = getInteractions(volufileMM)
+
+    volufileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_SM_"+pdbname+"_Repair_PN.txt"
+    wt_nvoSM = getInteractions(volufileSM)
+
+    volufileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_SS_"+pdbname+"_Repair_PN.txt"
+    wt_nvoSS = getInteractions(volufileSS)
+
+    dnc = []
+    dneRR = []
+    dneMM = []
+    dneSM = []
+    dneSS = [] 
+    dndRR = []
+    dndMM = []
+    dndSM = []
+    dndSS = []
+    dnhRR = []
+    dnhMM = []
+    dnhSM = []
+    dnhSS = []
+    dnpRR = []
+    dnpMM = []
+    dnpSM = []
+    dnpSS = []
+    dnvRR = []
+    dnvMM = []
+    dnvSM = []
+    dnvSS = []
+    dnvoRR = []
+    dnvoMM = []
+    dnvoSM = []
+    dnvoSS = []
+    for n in range(1, nmuts):
+        filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Distances_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
+        mut_nc = getInteractions(filename)
+        diffc = wt_nc - mut_nc
+        dnc.append(diffc)
+
+        filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
+        mut_neRR = getInteractions(filename)
+        diffeRR = wt_neRR - mut_neRR
+        dneRR.append(diffeRR)
+
+        filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
+        mut_ndRR = getInteractions(filename)
+        diffdRR = wt_ndRR - mut_ndRR
+        dndRR.append(diffdRR)
+ 
+        filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
+        mut_nhRR = getInteractions(filename)
+        diffhRR = wt_nhRR - mut_nhRR
+        dnhRR.append(diffhRR)
+        
+        filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
+        mut_npRR = getInteractions(filename)
+        diffpRR = wt_npRR - mut_npRR
+        dnpRR.append(diffpRR)
+
+        filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
+        mut_nvRR = getInteractions(filename)
+        diffvRR = wt_nvRR - mut_nvRR
+        dnvRR.append(diffvRR)
+
+        filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
+        mut_nvoRR = getInteractions(filename)
+        diffvoRR = wt_nvoRR - mut_nvoRR
+        dnvoRR.append(diffvoRR)
+    print(dnc)
+    print(dneRR)
+    print(dndRR)
+    print(dnhRR)
+    print(dnpRR)
+    print(dnvRR)
+    print(dnvoRR)
+
+    results = pd.DataFrame([(ddG),(dnc),(dneRR),(dndRR),(dnhRR),(dnpRR),(dnvRR),(dnvoRR)], columns=mutlist, index=["ddG","contacts","electro","disulfide","hbonds","partcov","VdWClashes","volumetric"])
+    results.append(ddG)
+    print(results)
+    results2 = results.T # transpose df
+    outputfilename = "foldx_results_"+pdbname+".csv"
+#    results.to_csv(outputfilename)
+    results2.to_csv(outputfilename)
+if __name__ == "__main__":
+    main()

foldx/test2/runPrintNetworks.sh

@@ -0,0 +1,7 @@
+PDB=$1
+n=$2
+OUTDIR=$3
+logger "Running runPrintNetworks"
+cd ${OUTDIR}
+ 
+foldx --command=PrintNetworks --pdb="${PDB}_Repair_${n}.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}

foldx/test2/runcomplex.sh

@@ -0,0 +1,9 @@
+PDB=$1
+A=$2
+B=$3
+OUTDIR=$4
+cd ${OUTDIR}
+logger "Running runcomplex"
+foldx --command=AnalyseComplex --pdb="${PDB}_Repair.pdb" --analyseComplexChains=${A},${B} --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}
+cp ${OUTDIR}/Summary_${PDB}_Repair_AC.fxout ${OUTDIR}/Summary_${PDB}_Repair_AC.txt
+#sed -i .bak -e 1,8d ${OUTDIR}/Summary_${PDB}_Repair_AC.txt 

foldx/test2/runfoldx.sh

@@ -0,0 +1,9 @@
+PDB=$1
+OUTDIR=$2
+cd ${OUTDIR}
+pwd
+ls -l
+logger "Running runfoldx"
+foldx --command=BuildModel --pdb="${PDB}_Repair.pdb" --mutant-file="individual_list_${PDB}.txt" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 --out-pdb=true --numberOfRuns=1 --output-dir=.
+foldx --command=PrintNetworks --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=.
+foldx --command=SequenceDetail --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=.

scripts/data_extraction.py

@@ -26,7 +26,7 @@ Created on Tue Aug  6 12:56:03 2019
 # 1) <gene>_gwas.csv
 # 2) <gene>_common_ids.csv
 # 3) <gene>_ambiguous_muts.csv
-# 4) <gene>_mcsm_snps.csv
+# 4) <gene>_mcsm_formatted_snps.csv
 # 5) <gene>_metadata_poscounts.csv
 # 6) <gene>_metadata.csv
 # 7) <gene>_all_muts_msa.csv
@@ -81,8 +81,8 @@ indir   = args.input_dir
 outdir  = args.output_dir
 make_dirs  = args.make_dirs
 
-#drug = 'ethambutol'
+#drug = 'streptomycin'
-#gene = 'embB'
+#gene = 'gid'
 
 #%% input and output dirs and files
 #=======
@@ -122,15 +122,15 @@ if make_dirs:
 # handle missing dirs here
 if not os.path.isdir(datadir):
     print('ERROR: Data directory does not exist:', datadir
-    , '\nPlease create and ensure gwas data is present and then rerun\nelse specify cmd option ---make_dirs')
+    , '\nPlease create and ensure gwas data is present and then rerun\nelse specify cmd option --make_dirs')
     sys.exit()
 if not os.path.isdir(indir):
     print('ERROR: Input directory does not exist:', indir
-    , '\nPlease either create or specify indir and rerun\nelse specify cmd option ---make_dirs')
+    , '\nPlease either create or specify indir and rerun\nelse specify cmd option --make_dirs')
     sys.exit()
 if not os.path.isdir(outdir):
     print('ERROR: Output directory does not exist:', outdir
-    , '\nPlease create or specify outdir and rerun\nelse specify cmd option ---make_dirs')
+    , '\nPlease create or specify outdir and rerun\nelse specify cmd option --make_dirs')
     sys.exit()
     
 # Requires
@@ -317,7 +317,7 @@ for i, id in enumerate(clean_df.id):
 print('RESULTS:')        
 print('Total WT in dr_muts_col:', wt)
 print('Total matches of', gene, 'SNP matches in', dr_muts_col, ':', dr_gene_count)
-print('Total samples with > 1', gene, 'muts in dr_muts_col:', len(id2_dr) )
+print('Total samples with > 1', gene, 'nsSNPs in dr_muts_col:', len(id2_dr) )
 print('=================================================================')
 
 del(clean_df, na_count, i, id, wt, id2_dr, count_gene_dr, count_wt)
@@ -361,7 +361,7 @@ for i, id in enumerate(clean_df.id):
 print('RESULTS:')
 print('Total WT in other_muts_col:', wt_other)
 print('Total matches of', gene, 'SNP matches in', other_muts_col, ':', other_gene_count)
-print('Total samples with > 1', gene, 'muts in other_muts_col:', len(id2_other) )
+print('Total samples with > 1', gene, 'nsSNPs in other_muts_col:', len(id2_other) )
 print('=================================================================')
 
 print('Predicting total no. of rows in the curated df:', dr_gene_count + other_gene_count
@@ -851,7 +851,7 @@ else:
           , '\nMuts are unique to dr_ and other_ mutation class'
           , '\n=========================================================')
 
-# inspect dr_muts and other muts    
+# inspect dr_muts and other muts: Fixed in case no ambiguous muts detected!
 if dr_muts.isin(other_muts).sum() & other_muts.isin(dr_muts).sum() > 0:
     print('Finding ambiguous muts...'
           , '\n========================================================='
@@ -860,24 +860,37 @@ if dr_muts.isin(other_muts).sum() & other_muts.isin(dr_muts).sum() > 0:
           , '\n========================================================='
           , '\nTotal no. of samples in other_muts present in dr_muts:', other_muts.isin(dr_muts).sum()
           , '\nThese are:\n', other_muts[other_muts.isin(dr_muts)]
-          , '\n=========================================================')    
+          , '\n=========================================================')
+    
+    print('Counting no. of ambiguous muts...'
+          , '\nNo. of ambiguous muts in dr:'
+          , len(dr_muts[dr_muts.isin(other_muts)].value_counts().keys().tolist())
+          , '\nNo. of ambiguous muts in other:'
+          , len(other_muts[other_muts.isin(dr_muts)].value_counts().keys().tolist())
+          , '\n=========================================================')
+    
+    if dr_muts[dr_muts.isin(other_muts)].nunique() == other_muts[other_muts.isin(dr_muts)].nunique(): 
+        common_muts = dr_muts[dr_muts.isin(other_muts)].value_counts().keys().tolist()
+        print('Distinct no. of ambigiuous muts detected:'+ str(len(common_muts))
+              , '\nlist of ambiguous mutations (see below):', *common_muts, sep = '\n')
+        print('\n===========================================================') 
 else:
-    sys.exit('Error: ambiguous muts present, but extraction failed. Debug!')
+    #sys.exit('Error: ambiguous muts present, but extraction failed. Debug!')
-
+    print('No: ambiguous muts present')
-print('Counting no. of ambiguous muts...') 
+    
-
+#print('Counting no. of ambiguous muts...')
-if dr_muts[dr_muts.isin(other_muts)].nunique() == other_muts[other_muts.isin(dr_muts)].nunique(): 
+#if dr_muts[dr_muts.isin(other_muts)].nunique() == other_muts[other_muts.isin(dr_muts)].nunique(): 
-    common_muts = dr_muts[dr_muts.isin(other_muts)].value_counts().keys().tolist()
+#    common_muts = dr_muts[dr_muts.isin(other_muts)].value_counts().keys().tolist()
-    print('Distinct no. of ambigiuous muts detected:'+ str(len(common_muts))
+#    print('Distinct no. of ambigiuous muts detected:'+ str(len(common_muts))
-          , '\nlist of ambiguous mutations (see below):', *common_muts, sep = '\n')
+#          , '\nlist of ambiguous mutations (see below):', *common_muts, sep = '\n')
-    print('\n===========================================================')
+#    print('\n===========================================================')
-else:
+#else:
-   print('Error: ambiguous muts detected, but extraction failed. Debug!'
+#   print('Error: ambiguous muts detected, but extraction failed. Debug!'
-         , '\nNo. of ambiguous muts in dr:'
+#         , '\nNo. of ambiguous muts in dr:'
-         , len(dr_muts[dr_muts.isin(other_muts)].value_counts().keys().tolist())
+#         , len(dr_muts[dr_muts.isin(other_muts)].value_counts().keys().tolist())
-         , '\nNo. of ambiguous muts in other:'
+#         , '\nNo. of ambiguous muts in other:'
-         , len(other_muts[other_muts.isin(dr_muts)].value_counts().keys().tolist())
+#         , len(other_muts[other_muts.isin(dr_muts)].value_counts().keys().tolist())
-         , '\n=========================================================')       
+#         , '\n=========================================================')       
          
 #%% clear variables
 del(id_dr, id_other
@@ -893,25 +906,24 @@ del(c1, c2, col_to_split1, col_to_split2, comp_gene_samples, dr_WF0, dr_df, dr_m
 #print(outdir)
 #dr_muts.to_csv('dr_muts.csv', header = True)
 #other_muts.to_csv('other_muts.csv', header = True)
+if dr_muts.isin(other_muts).sum() & other_muts.isin(dr_muts).sum() > 0:
+    out_filename_ambig_muts = gene.lower() + '_ambiguous_muts.csv'
+    outfile_ambig_muts = outdir + '/' + out_filename_ambig_muts
+    print('\n----------------------------------'
+          , '\nWriting file: ambiguous muts'
+          , '\n----------------------------------'
+          , '\nFilename:', outfile_ambig_muts)
+    inspect = gene_LF1[gene_LF1['mutation'].isin(common_muts)]
+    inspect.to_csv(outfile_ambig_muts, index = False)
 
-out_filename_ambig_muts = gene.lower() + '_ambiguous_muts.csv'
+    print('Finished writing:', out_filename_ambig_muts
-outfile_ambig_muts = outdir + '/' + out_filename_ambig_muts
+          , '\nNo. of rows:', len(inspect)
-print('\n----------------------------------'
+          , '\nNo. of cols:', len(inspect.columns)
-      , '\nWriting file: ambiguous muts'
+          , '\nNo. of rows = no. of samples with the ambiguous muts present:'
-      , '\n----------------------------------'
+          , dr_muts.isin(other_muts).sum() + other_muts.isin(dr_muts).sum()
-      , '\nFilename:', outfile_ambig_muts)
+          , '\n=============================================================')
+    del(out_filename_ambig_muts)
 
-inspect = gene_LF1[gene_LF1['mutation'].isin(common_muts)]
-inspect.to_csv(outfile_ambig_muts, index = False)
-
-print('Finished writing:', out_filename_ambig_muts
-      , '\nNo. of rows:', len(inspect)
-      , '\nNo. of cols:', len(inspect.columns)
-      , '\nNo. of rows = no. of samples with the ambiguous muts present:'
-      , dr_muts.isin(other_muts).sum() + other_muts.isin(dr_muts).sum()
-      , '\n=============================================================')
-      
-del(out_filename_ambig_muts)
 #%% end of data extraction and some files writing. Below are some more files writing.
 #=============================================================================
 #%% Formatting df: read aa dict and pull relevant info
@@ -1181,7 +1193,7 @@ if snps_only.mutationinformation.isna().sum() == 0:
 else:
     sys.exit('FAIL: SNP has NA, Possible mapping issues from dict?')
 
-out_filename_mcsmsnps = gene.lower() + '_mcsm_snps.csv'
+out_filename_mcsmsnps = gene.lower() + '_mcsm_formatted_snps.csv'
 outfile_mcsmsnps = outdir + '/' + out_filename_mcsmsnps
 
 print('\n----------------------------------'
@@ -1215,7 +1227,7 @@ metadata_pos.sort_values(by = ['meta_pos_count'], ascending = False, inplace = T
 out_filename_metadata_poscounts = gene.lower() + '_metadata_poscounts.csv'
 outfile_metadata_poscounts = outdir + '/' + out_filename_metadata_poscounts
 print('\n----------------------------------'
-      , 'Writing file: Metadata poscounts'
+      , '\nWriting file: Metadata poscounts'
       , '\n----------------------------------'
       , '\nFile:', outfile_metadata_poscounts
       , '\n============================================================')
@@ -1309,7 +1321,7 @@ out_filename_pos = gene.lower() + '_mutational_positons.csv'
 outfile_pos = outdir + '/' + out_filename_pos
 
 print('\n----------------------------------'
-      , 'Writing file: mutational positions'
+      , '\nWriting file: mutational positions'
       , '\n----------------------------------'
       , '\nFile:', outfile_pos
       , '\nNo. of distinct positions:', len(pos_only_sorted)
@@ -1349,15 +1361,14 @@ print('============================================'
       , '\nTotal no. of samples with missense muts:', len(gene_LF1)
       , '\nTotal no. of unique samples with missense muts:', gene_LF1['id'].nunique()  
       , '\n'
-      , '\nTotal no.of samples with common_ids:',  nu_common_ids['id']
+      , '\nTotal no.of samples with common_ids:',  nu_common_ids['id'])
-      , '\nTotal no.of samples with ambiguous muts:', len(inspect)
-      #, '\nTotal no.of unique ambiguous muts:', len(common_muts)
-      , '\nTotal no.of unique ambiguous muts:', inspect['mutation'].nunique()
-      , '\n============================================================='
-      , '\n\n\n')
-
-
 
+if dr_muts.isin(other_muts).sum() & other_muts.isin(dr_muts).sum() > 0:
+    print('\nTotal no.of samples with ambiguous muts:', len(inspect)
+          #, '\nTotal no.of unique ambiguous muts:', len(common_muts)
+          , '\nTotal no.of unique ambiguous muts:', inspect['mutation'].nunique()
+          , '\n============================================================='
+          , '\n\n\n')
 #=======================================================================
 print(u'\u2698' * 50,
       '\nEnd of script: Data extraction and writing files'

scripts/running_scripts

@@ -1,32 +1,42 @@
 #========
 # data extraction: Must be run first to extract mutations for each drug-gene combination
 #========
-./data_extraction.py -d pyrazinamide -g pncA 
+./data_extraction.py -d <drug> -g <gene> --make_dirs
+
+#========
+# add chains to a PDB file: for modeller models lack chain ID, this script is used
+#========
+add_chains_pdb.py <N> MY_PDB.pdb 
+
+#========
+# pdb data extraction: To find out discontinuity of chain and removing invalid muts to allow foldx and mcsm to run properly!
+#========
+In progress...
 
 #========
 # foldx: specify chain if default is NOT 'A'
 #========
-./runFoldx.py -d pyrazinamide -g pncA
+./runFoldx.py -d <drug> -g <gene> -c1 A -p /media/tanu/eb1d072a-3f73-427f-aeb8-f6852b5c5216/Data/processing
 
 #========
 # mcsm: specify chain if default is NOT 'A'
 #========
-./run_mcsm.py -d pyrazinamide -g pncA -s submit -l PZA --debug
+./run_mcsm.py -d <drug> -g <gene> -s submit -l PZA --debug
-./run_mcsm.py -d pyrazinamide -g pncA -s get
+./run_mcsm.py -d <drug> -g <gene> pncA -s get
-./run_mcsm.py -d pyrazinamide -g pncA -s format
+./run_mcsm.py -d <drug> -g <gene> pncA -s format
 
 #====================
 # other struct params
 #====================
-./dssp_df.py -d pyrazinamide -g pncA
+./dssp_df.py -d <drug> -g <gene>
 # Errors on matplot.lib warn=, so just comment it out for the timebeing!: MONKEY PATCH
-./kd_df.py -d pyrazinamide -g pncA  -fasta # fixme: NO of cols says 2, but is actually 3
+./kd_df.py -d <drug> -g <gene>  -fasta # fixme: NO of cols says 2, but is actually 3
-./rd_df.py -d pyrazinamide -g pncA # fixme: input tsv file is sourced manually from website!
+./rd_df.py -d <drug> -g <gene> # fixme: input tsv file is sourced manually from website!
 
 #==============================
 # af_or calcs: different types
 #==============================
-./af_or_calcs.R --d pyrazinamide --gene pncA # fixme: No conditional dir structure
+./af_or_calcs.R -d <drug> -g <gene># fixme: No conditional dir structure
 
 #==============================
 # af_or calcs: kinship
@@ -40,18 +50,18 @@ USE THE BELOW from within the or_kinship_link.py script or something?! as part o
 # for now use the file already created using some manual wrestling to link
 # the OR for kinship with mutations
 
-./or_kinship_link.py  -d pyrazinamide -g pncA -sc 2288681 -ec 2289241
+./or_kinship_link.py -d <drug> -g <gene> -sc <start_coord> -ec <end_coord>
 
 #==============================
 # formatting: ns<gene>_snp_info.txt
 #==============================
 # This adds mcsm style muts
-./snpinfo_format.py -d pyrazinamide -g pncA
+./snpinfo_format.py -d <drug> -g <gene>
 
 #==============================
 # combining dfs: combining_dfs.py
 #==============================
 # FIXME: combining_FIXME.py
-./combining_dfs.py -d pyrazinamide -g pncA
+./combining_dfs.py --d <drug> -g <gene>