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PlddtComparison.py
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PlddtComparison.py
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def PlddtComparison():
import math
import numpy as np
k=1
file5=open('SARS2-Caninef15LeftProteinList.tsv','r')
Title='E:\Research\\' + file5.name.replace('ProteinList.tsv', 'PercentDifference.tsv')
Title2='E:\Research\\' + file5.name.replace('ProteinList.tsv', 'RBDPercentDifference.tsv')
ProteinList=file5.readlines()
l=0
j=0
h=0
p=0
z=0
Quadrupletsperlist=int(len(ProteinList)/4)
WhichChimera='Chimera1'
if WhichChimera=='Chimera1' or 'Chimera2':
ArrayWidth=3
else:
ArrayWidth=6
print(WhichChimera)
PercentDifference=np.empty(((int(len(ProteinList)/4)),ArrayWidth), dtype=object)
PercentDifferenceRBD=np.empty(((int(len(ProteinList)/4)),ArrayWidth), dtype=object)
Plddtfiles=np.empty((len(ProteinList)), dtype=object)
for line in ProteinList:
x=line.split()
Plddtfiles[l]=''
Plddtfiles[l]=x[0]
for h in range(int(len(ProteinList)/4)):
PercentDifference[h]=''
PercentDifferenceRBD[h]=''
while k in range(Quadrupletsperlist):
file=open(Plddtfiles[0+j],"r")
file2=open(Plddtfiles[1+j],"r")
if WhichChimera=='Chimera1':
file3=open(Plddtfiles[2+j],"r")
file4 = open(Plddtfiles[2 + j], "r")
elif WhichChimera=='Chimera2':
file4=open(Plddtfiles[3+j],"r")
file3 = open(Plddtfiles[3 + j], "r")
else:
file3 = open(Plddtfiles[2 + j], "r")
file4=open(Plddtfiles[3+j],"r")
Score1=file.readlines()
Score2=file2.readlines()
Score3=file3.readlines()
Score4=file4.readlines()
LengthofProtein1=len(Score1)
LengthofProtein2=len(Score2)
LengthofChimera1=len(Score3)
i=0
Sumofnonsplice1=0
Sumofsplice1=0
while i in range(LengthofChimera1):
if i<(int(ProteinList[z+2].split()[1])):
Sumofnonsplice1+=float(Score3[i])
i+=1
elif (int(ProteinList[z+2].split()[2])+int(ProteinList[z+2].split()[1]))>i>=int(ProteinList[z+2].split()[1]):
Sumofsplice1+=float(Score3[i])
i+=1
elif i>= (int(ProteinList[z+2].split()[1])+int(ProteinList[z+2].split()[2])):
Sumofnonsplice1+=float(Score3[i])
i+=1
Averageofsplice1=(Sumofsplice1/int(ProteinList[z+2].split()[2]))
Averageofnonsplice1=(Sumofnonsplice1/(LengthofChimera1-int(ProteinList[z+2].split()[2])))
LengthofChimera2=len(Score4)
i=0
Sumofnonsplice2=0
Sumofsplice2=0
while i in range(LengthofChimera2):
if i<int(ProteinList[z+3].split()[1]):
Sumofnonsplice2+=float(Score4[i])
i+=1
elif (int(ProteinList[z+3].split()[2])+int(ProteinList[z+3].split()[1]))>i>=int(ProteinList[z+3].split()[1]):
Sumofsplice2+=float(Score4[i])
i+=1
elif i>= (int(ProteinList[z+3].split()[2])+int(ProteinList[z+3].split()[1])):
Sumofnonsplice2+=float(Score4[i])
i+=1
Averageofsplice2=(Sumofsplice2/int(ProteinList[z+3].split()[2]))
Averageofnonsplice2=(Sumofnonsplice2/(LengthofChimera2-int(ProteinList[z+3].split()[2])))
i=0
Sumofnonrbd2=0
Sumofrbd2=0
while i in range(LengthofProtein2):
if i<int(ProteinList[z+1].split()[1]):
Sumofnonrbd2+=float(Score2[i])
i+=1
elif (int(ProteinList[z+1].split()[1])+int(ProteinList[z+1].split()[2]))>i>=int(ProteinList[z+1].split()[1]):
Sumofrbd2+=float(Score2[i])
i+=1
elif i>= (int(ProteinList[z+1].split()[2])+int(ProteinList[z+1].split()[1])):
Sumofnonrbd2+=float(Score2[i])
i+=1
Averageofrbd2=(Sumofrbd2/int(ProteinList[z+1].split()[2]))
Averageofnonrbd2=(Sumofnonrbd2/(LengthofProtein2-int(ProteinList[z+2].split()[2])))
i=0
Sumofnonrbd1=0
Sumofrbd1=0
while i in range(LengthofProtein1):
if i<int(ProteinList[z].split()[1]):
Sumofnonrbd1+=float(Score1[i])
i+=1
elif (int(ProteinList[z].split()[2])+int(ProteinList[z].split()[1]))>i>=int(ProteinList[z].split()[1]):
Sumofrbd1+=float(Score1[i])
i+=1
elif i>= (int(ProteinList[z].split()[2])+int(ProteinList[z].split()[1])):
Sumofnonrbd1+=float(Score1[i])
i+=1
#how can i name this better with different situations?
Averageofrbd1=(Sumofrbd1/int(ProteinList[z].split()[2]))
Averageofnonrbd1=(Sumofnonrbd1/(LengthofProtein1-int(ProteinList[z].split()[2])))
Chimera1 = file3.name.replace('RBD.plddt', 'NonRBD')
Chimera1RBD = file3.name.replace('RBD.plddt', 'RBD')
Chimera2 = file4.name.replace('RBD.plddt', 'NonRBD')
Chimera2RBD = file4.name.replace('RBD.plddt', 'RBD')
Chimera1 = Chimera1.replace('E:\\Plddt\\', '')
Chimera1RBD = Chimera1RBD.replace('E:\\Plddt\\', '')
Chimera2 = Chimera2.replace('E:\\Plddt\\', '')
Chimera2RBD = Chimera2RBD.replace('E:\\Plddt\\', '')
DifferenceofNonRBD1Averages=((Averageofnonrbd1-Averageofnonsplice1)/Averageofnonrbd1)*100
DifferenceofRBD1Averages=((Averageofrbd2-Averageofsplice1)/Averageofrbd2)*100
DifferenceofNonRBD2Averages=((Averageofnonrbd2-Averageofnonsplice2)/Averageofnonrbd2)*100
DifferenceofRBD2Averages=((Averageofrbd1-Averageofsplice2)/Averageofrbd1)*100
if WhichChimera=='Chimera1':
PercentDifference[p,0]=Chimera1
PercentDifference[p,1]=DifferenceofNonRBD1Averages
PercentDifferenceRBD[p, 0] = Chimera1RBD
PercentDifferenceRBD[p, 1] = DifferenceofRBD1Averages
PercentDifferenceRBD[p, 2] = int(ProteinList[z + 2].split()[2])/(int(ProteinList[z + 2].split()[2])+int(ProteinList[z + 2].split()[1]))
np.savetxt(Title, PercentDifference, fmt="%s,%s,%s", delimiter=" ")
np.savetxt(Title2, PercentDifferenceRBD, fmt="%s,%s,%s", delimiter=" ")
elif WhichChimera=='Chimera2':
PercentDifference[p, 0] = Chimera2
PercentDifference[p, 1] = DifferenceofNonRBD2Averages
PercentDifferenceRBD[p, 0] = Chimera2RBD
PercentDifferenceRBD[p, 1] = DifferenceofRBD2Averages
np.savetxt(Title, PercentDifference, fmt="%s,%s,%s", delimiter=" ")
np.savetxt(Title2, PercentDifferenceRBD, fmt="%s,%s,%s", delimiter=" ")
else:
PercentDifference[p, 0] = Chimera1
PercentDifference[p, 1] = DifferenceofNonRBD1Averages
PercentDifferenceRBD[p, 0] = Chimera1RBD
PercentDifferenceRBD[p, 1] = DifferenceofRBD1Averages
PercentDifference[p, 2] = Chimera2
PercentDifference[p, 3] = DifferenceofNonRBD2Averages
PercentDifferenceRBD[p, 2] = Chimera2RBD
PercentDifferenceRBD[p, 3] = DifferenceofRBD2Averages
np.savetxt(Title, PercentDifference, fmt="%s,%s,%s,%s,%s,%s", delimiter=" ")
np.savetxt(Title2, PercentDifferenceRBD, fmt="%s,%s,%s,%s,%s,%s", delimiter=" ")
#PercentDifferenceRBD[p, 4] = int(ProteinList[z + 2].split()[2])
j += 4
p+=1
z+=4
print(PercentDifferenceRBD)