From 491b31775294725db332d25c498d9b28ec608623 Mon Sep 17 00:00:00 2001 From: Tanushree Tunstall Date: Wed, 10 Feb 2021 10:36:02 +0000 Subject: [PATCH] added depricated shell scripts --- .../mutrenamefiles_mac.sh | 68 ++++ .../deprecated_shell_scripts/mutruncomplex.sh | 10 + .../renamefiles_mac.sh | 68 ++++ foldx/deprecated_shell_scripts/repairPDB.sh | 9 + foldx/deprecated_shell_scripts/runFoldx.py | 336 ++++++++++++++++++ .../runPrintNetworks.sh | 7 + foldx/deprecated_shell_scripts/runcomplex.sh | 9 + foldx/deprecated_shell_scripts/runfoldx.sh | 9 + 8 files changed, 516 insertions(+) create mode 100755 foldx/deprecated_shell_scripts/mutrenamefiles_mac.sh create mode 100755 foldx/deprecated_shell_scripts/mutruncomplex.sh create mode 100755 foldx/deprecated_shell_scripts/renamefiles_mac.sh create mode 100755 foldx/deprecated_shell_scripts/repairPDB.sh create mode 100755 foldx/deprecated_shell_scripts/runFoldx.py create mode 100755 foldx/deprecated_shell_scripts/runPrintNetworks.sh create mode 100755 foldx/deprecated_shell_scripts/runcomplex.sh create mode 100755 foldx/deprecated_shell_scripts/runfoldx.sh diff --git a/foldx/deprecated_shell_scripts/mutrenamefiles_mac.sh b/foldx/deprecated_shell_scripts/mutrenamefiles_mac.sh new file mode 100755 index 0000000..b0e2fe9 --- /dev/null +++ b/foldx/deprecated_shell_scripts/mutrenamefiles_mac.sh @@ -0,0 +1,68 @@ +PDB=$1 +n=$2 +#cd /home/tanu/git/LSHTM_analysis/foldx/ +logger "Running mutrenamefiles_mac" +cp Matrix_Hbonds_${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_${n}_PN.txt +sed -i .bak -e 1,4d Matrix_Distances_${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_${n}_PN.txt +sed -i .bak -e 1,2d AllAtoms_Disulfide_${PDB}_Repair_${n}_PN.txt +cp AllAtoms_Electro_${PDB}_Repair_${n}_PN.fxout AllAtoms_Electro_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,2d AllAtoms_Electro_${PDB}_Repair_${n}_PN.txt +cp AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.fxout AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,2d AllAtoms_Hbonds_${PDB}_Repair_${n}_PN.txt +cp AllAtoms_Partcov_${PDB}_Repair_${n}_PN.fxout AllAtoms_Partcov_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,2d AllAtoms_Partcov_${PDB}_Repair_${n}_PN.txt +cp AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.fxout AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,2d AllAtoms_VdWClashes_${PDB}_Repair_${n}_PN.txt +cp AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.fxout AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,2d AllAtoms_Volumetric_${PDB}_Repair_${n}_PN.txt +cp InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.fxout InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,5d InteractingResidues_VdWClashes_${PDB}_Repair_${n}_PN.txt +cp InteractingResidues_Distances_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Distances_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,5d InteractingResidues_Distances_${PDB}_Repair_${n}_PN.txt +cp InteractingResidues_Electro_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Electro_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,5d InteractingResidues_Electro_${PDB}_Repair_${n}_PN.txt +cp InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,5d InteractingResidues_Hbonds_${PDB}_Repair_${n}_PN.txt +cp InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,5d InteractingResidues_Partcov_${PDB}_Repair_${n}_PN.txt +cp InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,5d InteractingResidues_Volumetric_${PDB}_Repair_${n}_PN.txt +cp InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.fxout InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.txt +sed -i .bak -e 1,5d InteractingResidues_Disulfide_${PDB}_Repair_${n}_PN.txt + + + + + + diff --git a/foldx/deprecated_shell_scripts/mutruncomplex.sh b/foldx/deprecated_shell_scripts/mutruncomplex.sh new file mode 100755 index 0000000..2b2c4e1 --- /dev/null +++ b/foldx/deprecated_shell_scripts/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 diff --git a/foldx/deprecated_shell_scripts/renamefiles_mac.sh b/foldx/deprecated_shell_scripts/renamefiles_mac.sh new file mode 100755 index 0000000..ea517bc --- /dev/null +++ b/foldx/deprecated_shell_scripts/renamefiles_mac.sh @@ -0,0 +1,68 @@ +PDB=$1 +logger "Running renamefiles_mac" +#cp Dif_${PDB}_Repair.fxout Dif_${PDB}_Repair.txt +sed -i '.bak' -e 1,8d Dif_${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 '.bak' -e 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_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,2d AllAtoms_Disulfide_${PDB}_Repair_PN.txt +cp AllAtoms_Electro_${PDB}_Repair_PN.fxout AllAtoms_Electro_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,2d AllAtoms_Electro_${PDB}_Repair_PN.txt +cp AllAtoms_Hbonds_${PDB}_Repair_PN.fxout AllAtoms_Hbonds_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,2d AllAtoms_Hbonds_${PDB}_Repair_PN.txt +cp AllAtoms_Partcov_${PDB}_Repair_PN.fxout AllAtoms_Partcov_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,2d AllAtoms_Partcov_${PDB}_Repair_PN.txt +cp AllAtoms_VdWClashes_${PDB}_Repair_PN.fxout AllAtoms_VdWClashes_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,2d AllAtoms_VdWClashes_${PDB}_Repair_PN.txt +cp AllAtoms_Volumetric_${PDB}_Repair_PN.fxout AllAtoms_Volumetric_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,2d AllAtoms_Volumetric_${PDB}_Repair_PN.txt +cp InteractingResidues_VdWClashes_${PDB}_Repair_PN.fxout InteractingResidues_VdWClashes_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,5d InteractingResidues_VdWClashes_${PDB}_Repair_PN.txt +cp InteractingResidues_Distances_${PDB}_Repair_PN.fxout InteractingResidues_Distances_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,5d InteractingResidues_Distances_${PDB}_Repair_PN.txt +cp InteractingResidues_Electro_${PDB}_Repair_PN.fxout InteractingResidues_Electro_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,5d InteractingResidues_Electro_${PDB}_Repair_PN.txt +cp InteractingResidues_Hbonds_${PDB}_Repair_PN.fxout InteractingResidues_Hbonds_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,5d InteractingResidues_Hbonds_${PDB}_Repair_PN.txt +cp InteractingResidues_Partcov_${PDB}_Repair_PN.fxout InteractingResidues_Partcov_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,5d InteractingResidues_Partcov_${PDB}_Repair_PN.txt +cp InteractingResidues_Volumetric_${PDB}_Repair_PN.fxout InteractingResidues_Volumetric_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,5d InteractingResidues_Volumetric_${PDB}_Repair_PN.txt +cp InteractingResidues_Disulfide_${PDB}_Repair_PN.fxout InteractingResidues_Disulfide_${PDB}_Repair_PN.txt +sed -i '.bak' -e 1,5d InteractingResidues_Disulfide_${PDB}_Repair_PN.txt + + + + + + diff --git a/foldx/deprecated_shell_scripts/repairPDB.sh b/foldx/deprecated_shell_scripts/repairPDB.sh new file mode 100755 index 0000000..ee1a13c --- /dev/null +++ b/foldx/deprecated_shell_scripts/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} diff --git a/foldx/deprecated_shell_scripts/runFoldx.py b/foldx/deprecated_shell_scripts/runFoldx.py new file mode 100755 index 0000000..2bf0067 --- /dev/null +++ b/foldx/deprecated_shell_scripts/runFoldx.py @@ -0,0 +1,336 @@ +#!/usr/bin/env python3 +import subprocess +import os +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 + + input') +arg_parser.add_argument('-o', '--output_dir', help = 'Output dir for results. By default, it assmes homedir + + output') +arg_parser.add_argument('-p', '--process_dir', help = 'Temp processing dir for running foldX. By default, it assmes homedir + + 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 _complex.pdb in input_dir') +arg_parser.add_argument('-m', '--mutation_file', help = 'Mutation list. By default, assumes a file called _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' + +#======= +# 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 = mut_filename +else: + mutation_file = gene.lower() + '_mcsm_formatted_snps.csv' + +infile_muts = outdir + '/' + mutation_file + +#======= +# 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 +, '\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() diff --git a/foldx/deprecated_shell_scripts/runPrintNetworks.sh b/foldx/deprecated_shell_scripts/runPrintNetworks.sh new file mode 100755 index 0000000..c2bebab --- /dev/null +++ b/foldx/deprecated_shell_scripts/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} diff --git a/foldx/deprecated_shell_scripts/runcomplex.sh b/foldx/deprecated_shell_scripts/runcomplex.sh new file mode 100755 index 0000000..0c0483d --- /dev/null +++ b/foldx/deprecated_shell_scripts/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 diff --git a/foldx/deprecated_shell_scripts/runfoldx.sh b/foldx/deprecated_shell_scripts/runfoldx.sh new file mode 100755 index 0000000..5a929ce --- /dev/null +++ b/foldx/deprecated_shell_scripts/runfoldx.sh @@ -0,0 +1,9 @@ +PDB=$1 +OUTDIR=$2 +cd ${OUTDIR} +pwd +ls +logger "Running runfoldx" +foldx --command=BuildModel --pdb="${PDB}_Repair.pdb" --mutant-file="individual_list_${PDB}.txt" --ionStrength=0.05 --pH=7 --water=PREDICT --vdwDesign=1 --out-pdb=true --numberOfRuns=1 --output-dir=${OUTDIR} +foldx --command=PrintNetworks --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR} +foldx --command=SequenceDetail --pdb="${PDB}_Repair.pdb" --water=PREDICT --vdwDesign=1 --output-dir=${OUTDIR}