test2 bugfixes
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13 changed files with 851 additions and 69 deletions
250
foldx/test2/runFoldx_test.py
Executable file
250
foldx/test2/runFoldx_test.py
Executable file
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#!/usr/bin/env python3
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import subprocess
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import os
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import numpy as np
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import pandas as pd
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from contextlib import suppress
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import re
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import csv
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def getInteractions(filename):
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data = pd.read_csv(filename, index_col=0, header =0, sep="\t")
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contactList = getIndexes(data,1)
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print(contactList)
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number = len(contactList)
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return number
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def formatMuts(mut_file,pdbname):
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with open(mut_file) as csvfile:
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readCSV = csv.reader(csvfile)
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muts = []
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for row in readCSV:
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mut = row[0]
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muts.append(mut)
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mut_list = []
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outfile = "/home/tanu/git/LSHTM_analysis/foldx/test2/individual_list_"+pdbname+".txt"
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with open(outfile, "w") as output:
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for m in muts:
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print(m)
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mut = m[:1]+'A'+m[1:]
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mut_list.append(mut)
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mut = mut + ";"
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print(mut)
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output.write(mut)
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output.write("\n")
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return mut_list
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def getIndexes(data, value):
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colnames = data.columns.values
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listOfPos = list()
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result = data.isin([value])
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result.columns=colnames
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seriesdata = result.any()
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columnNames = list(seriesdata[seriesdata==True].index)
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for col in columnNames:
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rows = list(result[col][result[col]==True].index)
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for row in rows:
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listOfPos.append((row,col))
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return listOfPos
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def loadFiles(df):
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# load a text file in to np matrix
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resultList = []
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f = open(df,'r')
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for line in f:
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line = line.rstrip('\n')
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aVals = line.split("\t")
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fVals = list(map(np.float32, sVals))
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resultList.append(fVals)
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f.close()
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return np.asarray(resultList, dtype=np.float32)
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#=======================================================================
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def main():
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pdbname = '3pl1'
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mut_filename = "pnca_muts_sample.csv"
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mutlist = formatMuts(mut_filename, pdbname)
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print(mutlist)
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nmuts = len(mutlist)+1
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print(nmuts)
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print(mutlist)
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print("start")
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output = subprocess.check_output(['bash', 'runfoldx.sh', pdbname])
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print("end")
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for n in range(1,nmuts):
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print(n)
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with suppress(Exception):
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subprocess.check_output(['bash', 'runPrintNetworks.sh', pdbname,str(n)])
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for n in range(1,nmuts):
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print(n)
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with suppress(Exception):
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subprocess.check_output(['bash', 'mutrenamefiles.sh', pdbname,str(n)])
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out = subprocess.check_output(['bash','renamefiles.sh',pdbname])
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dGdatafile = "/home/tanu/git/LSHTM_analysis/foldx/test2/Dif_"+pdbname+"_Repair.txt"
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dGdata = pd.read_csv(dGdatafile, sep="\t")
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print(dGdata)
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ddG=[]
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for i in range(0,len(dGdata)):
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ddG.append(dGdata['total energy'].loc[i])
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print(ddG)
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distfile = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Distances_"+pdbname+"_Repair_PN.txt"
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wt_nc = getInteractions(distfile)
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elecfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_RR_"+pdbname+"_Repair_PN.txt"
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wt_neRR = getInteractions(elecfileRR)
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elecfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_MM_"+pdbname+"_Repair_PN.txt"
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wt_neMM = getInteractions(elecfileMM)
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elecfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_SM_"+pdbname+"_Repair_PN.txt"
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wt_neSM = getInteractions(elecfileSM)
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elecfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_SS_"+pdbname+"_Repair_PN.txt"
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wt_neSS = getInteractions(elecfileSS)
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disufileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_RR_"+pdbname+"_Repair_PN.txt"
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wt_ndRR = getInteractions(disufileRR)
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disufileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_MM_"+pdbname+"_Repair_PN.txt"
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wt_ndMM = getInteractions(disufileMM)
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disufileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_SM_"+pdbname+"_Repair_PN.txt"
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wt_ndSM = getInteractions(disufileSM)
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disufileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_SS_"+pdbname+"_Repair_PN.txt"
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wt_ndSS = getInteractions(disufileSS)
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hbndfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_RR_"+pdbname+"_Repair_PN.txt"
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wt_nhRR = getInteractions(hbndfileRR)
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hbndfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_MM_"+pdbname+"_Repair_PN.txt"
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wt_nhMM = getInteractions(hbndfileMM)
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hbndfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_SM_"+pdbname+"_Repair_PN.txt"
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wt_nhSM = getInteractions(hbndfileSM)
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hbndfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_SS_"+pdbname+"_Repair_PN.txt"
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wt_nhSS = getInteractions(hbndfileSS)
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partfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_RR_"+pdbname+"_Repair_PN.txt"
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wt_npRR = getInteractions(partfileRR)
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partfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_MM_"+pdbname+"_Repair_PN.txt"
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wt_npMM = getInteractions(partfileMM)
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partfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_SM_"+pdbname+"_Repair_PN.txt"
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wt_npSM = getInteractions(partfileSM)
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partfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_SS_"+pdbname+"_Repair_PN.txt"
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wt_npSS = getInteractions(partfileSS)
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vdwcfileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_RR_"+pdbname+"_Repair_PN.txt"
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wt_nvRR = getInteractions(vdwcfileRR)
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vdwcfileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_MM_"+pdbname+"_Repair_PN.txt"
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wt_nvMM = getInteractions(vdwcfileMM)
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vdwcfileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_SM_"+pdbname+"_Repair_PN.txt"
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wt_nvSM = getInteractions(vdwcfileSM)
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vdwcfileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_SS_"+pdbname+"_Repair_PN.txt"
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wt_nvSS = getInteractions(vdwcfileSS)
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volufileRR = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_RR_"+pdbname+"_Repair_PN.txt"
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wt_nvoRR = getInteractions(volufileRR)
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volufileMM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_MM_"+pdbname+"_Repair_PN.txt"
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wt_nvoMM = getInteractions(volufileMM)
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volufileSM = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_SM_"+pdbname+"_Repair_PN.txt"
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wt_nvoSM = getInteractions(volufileSM)
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volufileSS = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_SS_"+pdbname+"_Repair_PN.txt"
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wt_nvoSS = getInteractions(volufileSS)
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dnc = []
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dneRR = []
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dneMM = []
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dneSM = []
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dneSS = []
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dndRR = []
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dndMM = []
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dndSM = []
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dndSS = []
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dnhRR = []
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dnhMM = []
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dnhSM = []
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dnhSS = []
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dnpRR = []
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dnpMM = []
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dnpSM = []
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dnpSS = []
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dnvRR = []
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dnvMM = []
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dnvSM = []
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dnvSS = []
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dnvoRR = []
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dnvoMM = []
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dnvoSM = []
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dnvoSS = []
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for n in range(1, nmuts):
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filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Distances_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
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mut_nc = getInteractions(filename)
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diffc = wt_nc - mut_nc
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dnc.append(diffc)
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filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Electro_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
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mut_neRR = getInteractions(filename)
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diffeRR = wt_neRR - mut_neRR
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dneRR.append(diffeRR)
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filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Disulfide_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
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mut_ndRR = getInteractions(filename)
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diffdRR = wt_ndRR - mut_ndRR
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dndRR.append(diffdRR)
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filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Hbonds_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
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mut_nhRR = getInteractions(filename)
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diffhRR = wt_nhRR - mut_nhRR
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dnhRR.append(diffhRR)
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filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Partcov_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
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mut_npRR = getInteractions(filename)
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diffpRR = wt_npRR - mut_npRR
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dnpRR.append(diffpRR)
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filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_VdWClashes_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
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mut_nvRR = getInteractions(filename)
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diffvRR = wt_nvRR - mut_nvRR
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dnvRR.append(diffvRR)
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filename = "/home/tanu/git/LSHTM_analysis/foldx/test2/Matrix_Volumetric_RR_"+pdbname+"_Repair_" + str(n)+"_PN.txt"
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mut_nvoRR = getInteractions(filename)
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diffvoRR = wt_nvoRR - mut_nvoRR
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dnvoRR.append(diffvoRR)
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print(dnc)
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print(dneRR)
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print(dndRR)
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print(dnhRR)
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print(dnpRR)
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print(dnvRR)
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print(dnvoRR)
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results = pd.DataFrame([(ddG),(dnc),(dneRR),(dndRR),(dnhRR),(dnpRR),(dnvRR),(dnvoRR)], columns=mutlist, index=["ddG","contacts","electro","disulfide","hbonds","partcov","VdWClashes","volumetric"])
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results.append(ddG)
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print(results)
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results2 = results.T # transpose df
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outputfilename = "foldx_results_"+pdbname+".csv"
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# results.to_csv(outputfilename)
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results2.to_csv(outputfilename)
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if __name__ == "__main__":
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main()
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