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Added DNA sequences in SBOL #5

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Jul 26, 2020
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Added DNA sequences in SBOL #5

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341 changes: 341 additions & 0 deletions Debug.csv
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6 changes: 3 additions & 3 deletions python-only/Data.txt
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
c'(ab+b')
b(a'c'+c)
4
(c+(b'+a)')'
(Arabinose+(aTc'+IPTG)')'
(b'+(c+a')')'
(aTc'+(Arabinose+IPTG')')'
2 changes: 1 addition & 1 deletion python-only/Genetech.py
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Expand Up @@ -223,7 +223,7 @@ def saveImageDialog(self):
QMessageBox.about(self, "Alert", "A file name can't contain any of the following \n \ / : * ? < > |")
else:
item = self.CircuitList.currentItem() #the selected item
saveimg = Image.open(str(item.text())+".png") #use this image to save
saveimg = Image.open('user_files/'+str(item.text())+".png") #use this image to save
saveimg.save(str(UserfileName)+".png") #save image as

#or "?" in UserfileName or "/" in UserfileName or "*" in UserfileName or "<" in UserfileName or ">" in UserfileName or "|" in UserfileName or '"' in UserfileName:
Expand Down
157 changes: 129 additions & 28 deletions python-only/SBOL_File.py
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Original file line number Diff line number Diff line change
@@ -1,12 +1,37 @@
from sbol2 import *
from functions import *
import pandas as pd

class SBOL_File:
def __init__(self, total_gates, total_time, option, num):
DeleteExistingFiles()
circuits = ReadFile()
Component_strings = self.ListOfLines(circuits)
self.geneticPartsDf = None #dataframe containing information of genetic parts such as DNA sequence
self.gateRBS = {} #gets rbs corresponding to the gate
self.readGeneticParts()
self.gateRBSMapping()
self.CreateFile(Component_strings, len(Component_strings), total_gates, total_time, option, num)

def readGeneticParts(self):
"""
This function loads the csv file genetic_parts.csv into a
pandas dataframe for better access when adding sequences
"""
self.geneticPartsDf = pd.read_csv("genetic_parts.csv")


def gateRBSMapping(self):
"""
This function creates a mapping between a gate and it's corresponding
RBS (AmeR is mappedd to A1, PhlF mapped to P1, and so on) as given in the
genetic_parts.csv file
"""
listGates = self.geneticPartsDf.loc[self.geneticPartsDf.type == "CDS"].part
for i in listGates:
if i != "YFP":
rbs = self.geneticPartsDf.loc[self.geneticPartsDf.gate == i].part.values[0]
self.gateRBS[i] = rbs

def ListOfLines(self, circuits):
#This function filters out the unwanted characters from every line of each circuit
Expand All @@ -25,7 +50,6 @@ def ListOfLines(self, circuits):
return Component_strings

def CreateFile(self, input_list, circuits, total_gates, total_time, option, num):

for i in range(circuits): #iter for each circuit
file_num = SortNum(i, option) + 1
if Total_Gates(i) <= total_gates and Total_time(i) <= total_time and file_num <= num: #If Total Delay and number of gates are less than the input
Expand All @@ -38,43 +62,96 @@ def CreateFile(self, input_list, circuits, total_gates, total_time, option, num)
componentDef_string = [] #A list to contain name of the objects
count=1 #A variable to assign number to terminators

#Create ComponentDefinition for the whole Device which will contain the Components of each part and the SequenceConstraints
Device = ComponentDefinition('Output_Device_' + str(i+1))
Device.name = 'Output_Device ' + str(i+1) + ' Component'
doc.addComponentDefinition(Device)

#Create ModuleDefinition of the device, which will contain the FunctionalComponent of the device connected to its ComponentDefinition
Circuit = ModuleDefinition('Output_Circuit_' + str(i+1))
Circuit.name = 'Output Circuit Module'
doc.addModuleDefinition(Circuit)

#Create ComponentDefinition for the whole Device which will contain the Components of each part and the SequenceConstraints
Device = ComponentDefinition('Output_Device_' + str(i+1))
Device.name = 'Output_Device ' + str(i+1) + ' Component'
doc.addComponentDefinition(Device)


Circuit_fc = Circuit.functionalComponents.create('Device')
Circuit_fc.name = 'Device'
#This Functional Component needs a unique ID of the part it belongs to, in this case it belongs to the Device itself
Circuit_fc.definition = Device.identity
Circuit_fc.access = SBOL_ACCESS_PUBLIC
Circuit_fc.direction = SBOL_DIRECTION_NONE


### Terminator ###
terminator = self.geneticPartsDf.loc[self.geneticPartsDf.type == "Terminator"]
terminatorName = terminator.part.values[0]
terminatorSeq = terminator.sequence.values[0]
terminatorSeqObj = Sequence(terminatorName+"_sequence", terminatorSeq)

sequences = [terminatorSeqObj] #these will be added later to the doc
finalSequenceList = []
Terminator = ComponentDefinition(terminatorName, BIOPAX_DNA)
Terminator.roles = SO_TERMINATOR
Terminator.sequence = terminatorSeqObj
doc.addComponentDefinition(Terminator)

for j in range(len(input_list[i])): #iter for each line of the circuit
splitted_components = input_list[i][j].split() #each part in a line
name_line = [] #List to contain names of each part
def_line = [] #List to contain Component Definitions of each part
for k in range(len(splitted_components)): #Loop to get the individual names of promotors and coding sequences in the list
if splitted_components[k][0] == '(': #if the part is a coding sequence
Comp = ComponentDefinition(splitted_components[k][1:-1], BIOPAX_DNA)
name = splitted_components[k][1:-1]
Comp = ComponentDefinition(name, BIOPAX_DNA)
Comp.roles = SO_CDS
seqCDS = self.geneticPartsDf.loc[self.geneticPartsDf.part == name]
#print(name, seqCDS)
seqName = seqCDS.part.values[0]
seqValue = seqCDS.sequence.values[0]
seqObj = Sequence(seqName+"_sequence", seqValue)
sequences.append(seqObj)
Comp.sequence = seqObj

if name != "YFP":
rbs = self.gateRBS[name]
seqCDS = self.geneticPartsDf.loc[self.geneticPartsDf.part == rbs]
seqName = seqCDS.part.values[0]
seqValue = seqCDS.sequence.values[0]
seqObj = Sequence(seqName+"_sequence", seqValue)
sequences.append(seqObj)
RBS = ComponentDefinition(rbs, BIOPAX_DNA)
RBS.roles = SO_RBS
RBS.sequence = seqObj

doc.addComponentDefinition(RBS)

def_line.append(RBS)
name_line.append(rbs)

def_line.append(Comp)
name_line.append(splitted_components[k])

Terminator = ComponentDefinition('Terminator' + str(count), BIOPAX_DNA)
Terminator = ComponentDefinition(terminatorName+"__"+str(count), BIOPAX_DNA)
Terminator.roles = SO_TERMINATOR
doc.addComponentDefinition(Terminator)
Terminator.sequence = terminatorSeqObj
def_line.append(Terminator)
name_line.append('Terminator' + str(count))
name_line.append(terminatorName+"__"+str(count))

#Terminator = ComponentDefinition('Terminator' + str(count), BIOPAX_DNA)
#Terminator.roles = SO_TERMINATOR
#doc.addComponentDefinition(Terminator)
#def_line.append(Terminator)
#name_line.append('Terminator' + str(count))
count+=1
else:
Comp = ComponentDefinition(splitted_components[k], BIOPAX_DNA)
Comp.roles = SO_PROMOTER
seqCDS = self.geneticPartsDf.loc[self.geneticPartsDf.part == splitted_components[k]]
#print(name, seqCDS)
seqName = seqCDS.part.values[0]
seqValue = seqCDS.sequence.values[0]
seqObj = Sequence(seqName+"_sequence", seqValue)
sequences.append(seqObj)
Comp.sequence = seqObj

def_line.append(Comp)
name_line.append(splitted_components[k])

Expand All @@ -83,6 +160,20 @@ def CreateFile(self, input_list, circuits, total_gates, total_time, option, num)
component_defs.append(def_line)
componentDef_string.append(name_line)

#if circuit has 2 lines, add the 2nd line to the start of the first to match sbol visaul
if len(component_defs) > 1:
finalComp = component_defs[1][:]
finalCompString = componentDef_string[1][:]
finalComp.extend(component_defs[0][:])
finalCompString.extend(componentDef_string[0][:])
else:
finalComp = component_defs[0][:]
finalCompString = componentDef_string[0][:]
#print(finalComp)
#print(componentDef_string)
#print(finalCompString)
Device.assemblePrimaryStructure(finalComp)
print("DNA : ", Device.compile())
#For the Flourescent Protein, which is the last element of the first line of the circuit
FP_protein = ComponentDefinition(componentDef_string[0][-2][1:-1]+'_Protein', BIOPAX_PROTEIN)
doc.addComponentDefinition(FP_protein)
Expand All @@ -95,32 +186,40 @@ def CreateFile(self, input_list, circuits, total_gates, total_time, option, num)
for j in range(len(componentDef_string)): #This loop creates those Components
Components_line = []
for k in range(len(componentDef_string[j])):
name = componentDef_string[j][k] + "_component"

if componentDef_string[j][k][0] == '(':
name_c = Device.components.create(componentDef_string[j][k][1:-1])
else:
name_c = Device.components.create(componentDef_string[j][k])
name = componentDef_string[j][k][1:-1] + "_component"

name_c = Device.components.create(name)
name_c.definition = component_defs[j][k].identity
name_c.access = SBOL_ACCESS_PUBLIC
Components_line.append(name_c)

Components.append(Components_line)

s_contraint_list = []
for j in range(len(componentDef_string)): #This loop is to create the SequenceConstraints class to defines the Orientation of the device
for k in range(len(componentDef_string[j])-1):

if componentDef_string[j][k+1][0] == '(':
S_constraint = Device.sequenceConstraints.create(componentDef_string[j][k] + '_precedes_' + componentDef_string[j][k+1][1:-1])
name = componentDef_string[j][k] + '_precedes_' + componentDef_string[j][k+1][1:-1]
#S_constraint = Device.sequenceConstraints.create(componentDef_string[j][k] + '_precedes_' + componentDef_string[j][k+1][1:-1])

elif componentDef_string[j][k][0] == '(':
S_constraint = Device.sequenceConstraints.create(componentDef_string[j][k][1:-1] + '_precedes_' + componentDef_string[j][k+1])
name = componentDef_string[j][k][1:-1] + '_precedes_' + componentDef_string[j][k+1]
#S_constraint = Device.sequenceConstraints.create(componentDef_string[j][k][1:-1] + '_precedes_' + componentDef_string[j][k+1])

else:
S_constraint = Device.sequenceConstraints.create(componentDef_string[j][k] + '_precedes_' + componentDef_string[j][k+1])

name = componentDef_string[j][k] + '_precedes_' + componentDef_string[j][k+1]
#S_constraint = Device.sequenceConstraints.create(componentDef_string[j][k] + '_precedes_' + componentDef_string[j][k+1])

S_constraint.subject = Components[j][k].identity #Subject is the part that comes first
S_constraint.object = Components[j][k+1].identity #Object is the part that comes later
S_constraint.restriction = SBOL_RESTRICTION_PRECEDES #This describes the order we have defined for this Constraint
if name not in s_contraint_list:
s_contraint_list.append(name)
S_constraint = Device.sequenceConstraints.create(name)
S_constraint.subject = Components[j][k].identity #Subject is the part that comes first
S_constraint.object = Components[j][k+1].identity #Object is the part that comes later
S_constraint.restriction = SBOL_RESTRICTION_PRECEDES #This describes the order we have defined for this Constraint

if j == 0 and componentDef_string[j][k][0] == '(': #for the coding sequences in the first line of the circuit
#For the Module Definition, we only need the coding sequence and the output promotor
Expand Down Expand Up @@ -200,8 +299,9 @@ def CreateFile(self, input_list, circuits, total_gates, total_time, option, num)
S_constraint.restriction = SBOL_RESTRICTION_PRECEDES

if componentDef_string[j][k][0] == '(':
cds_fc = Circuit.functionalComponents.create(componentDef_string[j][1][1:-1])
cds_fc.definition = component_defs[j][1].identity
print("BUG HERE") # componentDef_string[j][1] instead of componentDef_string[j][k]
cds_fc = Circuit.functionalComponents.create(componentDef_string[j][k][1:-1])
cds_fc.definition = component_defs[j][k].identity
cds_fc.access = SBOL_ACCESS_PUBLIC
cds_fc.direction = SBOL_DIRECTION_NONE

Expand Down Expand Up @@ -262,9 +362,10 @@ def CreateFile(self, input_list, circuits, total_gates, total_time, option, num)
P_map.refinement = SBOL_REFINEMENT_USE_REMOTE
P_map.local = P_fc.identity
P_map.remote = Components[1][index_of_myP].identity

result = doc.write("user_files/SBOL File " + str(file_num) +".xml") #To save the SBOL File
print("here")
result = doc.write("user_files/"+"SBOL File " + str(file_num) +".xml") #To save the SBOL File
print("here ", result)

if __name__ == '__main__':
inputExp = "IPTG'.aTc'.Arabinose'+IPTG'.aTc.Arabinose'+IPTG.aTc'.Arabinose'"
#inputExp = "IPTG'.aTc'.Arabinose'+IPTG'.aTc.Arabinose'+IPTG.aTc'.Arabinose'"
f = SBOL_File(1000, 1000)
6 changes: 4 additions & 2 deletions python-only/circuits.txt
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Original file line number Diff line number Diff line change
@@ -1,8 +1,10 @@
******************* Genetic Circuit 1 *****************

PTet-> (AmtR) ----|PAmtR-> PTac-> (HlYllR) ----|PHlYllR-> PBad-> (BM3R1) ----|PBM3R1-> (YFP)
PTac-> (HlYllR) ----|PHlYllR-> PBad-> (AmtR) ----|PAmtR-> PAmeR-> (Betl) ----|PBetl-> (YFP)
PTet-> (AmeR)-----------------------------------------------^

******************* Genetic Circuit 2 *****************

PTet-> (AmtR) ----|PAmtR-> PTac-> (HlYllR) ----|PHlYllR-> PBad-> (SrpR) ----|PSrpR-> (YFP)
PTac-> (HlYllR) ----|PHlYllR-> PBad-> (SrpR) ----|PSrpR-> PAmtR-> (PhlF) ----|PPhlF-> (YFP)
PTet-> (AmtR)-----------------------------------------------^

11 changes: 9 additions & 2 deletions python-only/functions.py
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Original file line number Diff line number Diff line change
@@ -1,3 +1,7 @@
from sbol2 import *
#
import sbol2
print(sbol2.__version__)
import glob, os

def baseList():
Expand Down Expand Up @@ -85,12 +89,14 @@ def Delay(promotor1, CDS, promotor2 = None):
return Check_NOR(promotor1, promotor2, Output_P, Gates[3])
else:
return Check_NOR(promotor1, promotor2, Output_P, Gates[4])

return 0

def Check_NOT(promotor, Output_P, Gates):
"""Check the whole list and returns the delay of the gate matching with inputs"""
for i in Gates:
if i[0] == promotor and i[1] == Output_P:
return i[2]
return 0

def Check_NOR(promotor1, promotor2, Output_P, Gates):
"""Check the whole list and returns the delay of the gate matching with inputs"""
Expand All @@ -100,7 +106,8 @@ def Check_NOR(promotor1, promotor2, Output_P, Gates):
return i[3]
elif i[0] == promotor2 and i[1] == promotor1 and i[2] == Output_P: #e.g. if P1=PBetl and P2=PAmtR
return i[3]

return 0

def GatherGates():
f = open("GatesLib.txt")
lst = []
Expand Down
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