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ErrorModelMaker.py
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ErrorModelMaker.py
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import random, math
from sys import float_info
from Logger import Logger
import numpy as np
class ErrorModelMaker:
def __init__(self,
BuildInsertion = True,
BuildSubstitution = True,
BuildDeletion = True,
Variation = False,
FileName = None,
N=100,
DeletionPoints=[0.00606508512067950,0.00675296642376962,0.00688999694872917,0.00580692396866418,0.00680583604896024,0.00609061670962565,0.00585881991631447,0.00577148570812953,0.00600882981888663,0.00618499536435559,0.00650767341787896,0.00670521809234427,0.00699374780209504,0.00841141135948587,0.00830145870238677,0.00879477131238090,0.00918627324146331,0.00958946761973615,0.01032404247887830,0.01093417870737930,0.01188202458790520,0.01261860720648550,0.01355451051017660,0.01473818756656830,0.01623978223562570,0.01811682034513980,0.01990010225231130,0.02154250858435480,0.02418185925226890,0.02583490296173980,0.02844212438633430,0.03194935989118780,0.03534228607419560,0.03971366519834600,0.04548573525944540,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660],
InsertionPoints=[0.00606508512067950,0.00675296642376962,0.00688999694872917,0.00580692396866418,0.00680583604896024,0.00609061670962565,0.00585881991631447,0.00577148570812953,0.00600882981888663,0.00618499536435559,0.00650767341787896,0.00670521809234427,0.00699374780209504,0.00841141135948587,0.00830145870238677,0.00879477131238090,0.00918627324146331,0.00958946761973615,0.01032404247887830,0.01093417870737930,0.01188202458790520,0.01261860720648550,0.01355451051017660,0.01473818756656830,0.01623978223562570,0.01811682034513980,0.01990010225231130,0.02154250858435480,0.02418185925226890,0.02583490296173980,0.02844212438633430,0.03194935989118780,0.03534228607419560,0.03971366519834600,0.04548573525944540,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660],
SubstitutionPoints =[0.00606508512067950,0.00675296642376962,0.00688999694872917,0.00580692396866418,0.00680583604896024,0.00609061670962565,0.00585881991631447,0.00577148570812953,0.00600882981888663,0.00618499536435559,0.00650767341787896,0.00670521809234427,0.00699374780209504,0.00841141135948587,0.00830145870238677,0.00879477131238090,0.00918627324146331,0.00958946761973615,0.01032404247887830,0.01093417870737930,0.01188202458790520,0.01261860720648550,0.01355451051017660,0.01473818756656830,0.01623978223562570,0.01811682034513980,0.01990010225231130,0.02154250858435480,0.02418185925226890,0.02583490296173980,0.02844212438633430,0.03194935989118780,0.03534228607419560,0.03971366519834600,0.04548573525944540,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660,0.05190994307855660]):
"""
BuildInsertion = Do you want to build Insertion Errors?
BuildDeletion = Do you want to build Deletion Errors?
BuildSubstitution = Do you want to build Sustitution Errors?
(Required) Variation = Do you want to randomly vary the Error Rates
(Required)FileName = The name of the mconf file for the error model
DeletionPoints = The array of deletion rate values
InsertionPoints = The array of insertion rate values
SubstitutionPoints = The array of Substituion rate values
"""
self.SetDeletionPoints(DeletionPoints)
self.SetInsertionPoints(InsertionPoints)
self.SetSubstitutionPoints(SubstitutionPoints)
self.SetN(N)
self.SetBuildInsertion(BuildInsertion)
self.SetBuildSubstitution(BuildSubstitution)
self.SetBuildDeletion(BuildDeletion)
self.SetVariation(Variation)
if FileName == None:
FileName = 'ErrorModel-%dbp.mconf' %self.N
self.BuildErrorModel(FileName,self.N)
def SetDeletionPoints(self,Pts):
self.DeletionPoints = Pts
def SetInsertionPoints(self,Pts):
self.InsertionPoints = Pts
def SetSubstitutionPoints(self,Pts):
self.SubstitutionPoints = Pts
def SetN(self,N):
self.N= N
def SetVariation(self,X):
self.Variation = X
def SetBuildInsertion(self,Bool):
self.BuildInsertion = Bool
def SetBuildSubstitution(self,Bool):
self.BuildSubstitution = Bool
def SetBuildDeletion(self,Bool):
self.BuildDeletion = Bool
def GetVariation(self):
return self.Variation
def GetDeletionPoints(self):
return self.DeletionPoints
def GetInsertionPoints(self):
return self.InsertionPoints
def GetSubstitutionPoints(self):
return self.SubstitutionPoints
def GetN(self):
return self.N
def GetBuildInsertion(self):
return self.BuildInsertion
def GetBuildSubstitution(self):
return self.BuildSubstitution
def GetBuildDeletion(self):
return self.BuildDeletion
def Normalize(self,X):
"""
Input: X - an iterable, such as a list or tuple
output is normalized vector with unit magnitude
"""
NumpyX = np.array([float(i) for i in X])
Norm = np.linalg.norm(NumpyX,ord=1)
Normalize = NumpyX/Norm
if sum(Normalize)<1.0:
delta = 1.0-sum(Normalize)
partitionedDelta = delta/len(Normalize)
Normalize = np.array([X + partitionedDelta for X in Normalize])
elif sum(Normalize) > 1.0:
delta = sum(Normalize) - 1.0
partitionedDelta = delta/len(Normalize)
Normalize = np.array([X - partitionedDelta for X in Normalize])
return Normalize
def BuildErrorModel(self,FileName,N):
# Del = self.Normalize(self.GetDeletionPoints())
# Ins = self.Normalize(self.GetInsertionPoints())
# Sub = self.Normalize(self.GetSubstitutionPoints())
# self.SetDeletionPoints(Del)
# self.SetInsertionPoints(Ins)
# self.SetSubstitutionPoints(Sub)
File = open(FileName,'w')
self.BuildHeader(File)
self.BuildSwitches(File)
self.BuildDeletionErrors(File)
self.BuildSubstitutionErrors(File)
self.BuildInsertionErrors(File)
File.close()
def BuildHeader(self,FilePtr):
Logr = Logger()
TimeString = '#Date of Creation: %s\n'%Logr.TimeStamp2String(Logr.GetTimeStamp())
strings = ['#Error Model written by Pyllumina 2.1\n',TimeString]
FilePtr.writelines(strings)
def BuildSwitches(self,FilePtr):
BasePoints = ['G','T','A','C']
for k in range(len(BasePoints)):
X1 = BasePoints[k]
for j in range(len(BasePoints)):
X2 = BasePoints[j]
SwitchVector = self.Normalize([random.uniform(.3,.4+float_info.epsilon),random.uniform(.3,.4+float_info.epsilon),random.uniform(.3,.4+float_info.epsilon)])
Statement = '# (Set switch rates for %s following %s)\n' % (X1,X2)
FilePtr.write(Statement)
count = 0
for i in range(len(BasePoints)):
X3 = BasePoints[i]
if X3 == X2:
continue
else:
SwitchValue = SwitchVector[count]
count = count + 1
Statement = '%s(%s,%s) %f\n'%(X1,X2,X3,SwitchValue)
FilePtr.write(Statement)
count = 0 #reset count for next loop
def BuildSubstitutionErrors(self,FilePtr):
if self.GetBuildSubstitution() == True:
Points = self.GetSubstitutionPoints()
LastPtIndex = len(Points)-1
BasePoints = ['G','T','A','C']
for j in BasePoints:
Statement = '# Set Substitution Rates for every %s \n'% j
FilePtr.write(Statement)
Statement = 'SUBSTITUTION_ERROR (%s)\n' % j
FilePtr.write(Statement)
for i in range(self.GetN()):
if i <= LastPtIndex and self.GetVariation() == False:
Statement = '%.47f\n'%Points[i]
FilePtr.write(Statement)
elif i <= LastPtIndex and self.GetVariation() == True:
Statement = '%.47f\n'%(Points[i] + random.gauss(0,.00025))
FilePtr.write(Statement)
elif i >= LastPtIndex and self.GetVariation() == False:
Statement = '%.47f\n'%Points[LastPtIndex]
FilePtr.write(Statement)
else:
Statement = '%.47f\n'%(Points[LastPtIndex]+random.gauss(0,.00025))
FilePtr.write(Statement)
return
else:
return
def BuildInsertionErrors(self,FilePtr):
if self.GetBuildSubstitution() == True:
Points = self.GetInsertionPoints()
LastPtIndex = len(Points)-1
BasePoints = ['G','T','A','C']
for j in BasePoints:
Statement = '# Set Insertion Rates for every %s \n'% j
FilePtr.write(Statement)
Statement = 'INSERTION_ERROR (%s)\n' % j
FilePtr.write(Statement)
for i in range(self.GetN()):
if i <= LastPtIndex and self.GetVariation() == False:
Statement = '%.47f\n'%Points[i]
FilePtr.write(Statement)
elif i <= LastPtIndex and self.GetVariation() == True:
Statement = '%.47f\n'%(Points[i] + random.gauss(0,.00025))
FilePtr.write(Statement)
elif i >= LastPtIndex and self.GetVariation() == False:
Statement = '%.47f\n'%Points[LastPtIndex]
FilePtr.write(Statement)
else:
Statement = '%.47f\n'%(Points[LastPtIndex]+random.gauss(0,.00025))
FilePtr.write(Statement)
return
else:
return
def BuildDeletionErrors(self,FilePtr):
if self.GetBuildDeletion() == True:
Points = self.GetDeletionPoints()
LastPtIndex = len(Points)-1
BasePoints = ['G','T','A','C']
for j in BasePoints:
Statement = '# Set Deletion Rates for every %s \n'% j
FilePtr.write(Statement)
Statement = 'DELETION_ERROR (%s)\n' % j
FilePtr.write(Statement)
for i in range(self.GetN()):
if i <= LastPtIndex and self.GetVariation() == False:
Statement = '%.47f\n'%Points[i]
FilePtr.write(Statement)
elif i <= LastPtIndex and self.GetVariation() == True:
Statement = '%.47f\n'%(Points[i] + random.gauss(0,.00025))
FilePtr.write(Statement)
elif i >= LastPtIndex and self.GetVariation() == False:
Statement = '%.47f\n'%Points[LastPtIndex]
FilePtr.write(Statement)
else:
Statement = '%.47f\n'%(Points[LastPtIndex]+random.gauss(0,.00025))
FilePtr.write(Statement)
return
else:
return