def test_basic_RBS_CDS_RNAconstruct():
R = RBS("rbs")
C = CDS("gfp")
parameters={"cooperativity":2,"kb":100, "ku":10, "ktx":.05, "ktl":.2, "kdeg":2,"kint":.05}
mechs = {"translation":Translation_MM(Species("Ribo"))}
#minimal RNA translation
x = RNA_construct([R,C],mechanisms = mechs,parameters=parameters)
y = x.enumerate_components()
assert(x[0] ==y[0])
assert(y[1].protein==Species("gfp",material_type="protein"))
assert(y[0].transcript.parent==x.get_species())
#minimal RNA transcription
x = RNA_construct([C,R],mechanisms = mechs,parameters=parameters)
y = x.enumerate_components()
assert(y==[x[1]])
assert(y[0].transcript.parent==x.get_species())
#minimal RNA transcription
x = RNA_construct([[R,"reverse"],C],mechanisms = mechs,parameters=parameters)
y = x.enumerate_components()
assert(y==[])
#minimal RNA transcription
x = RNA_construct([R,[C,"reverse"]],mechanisms = mechs,parameters=parameters)
y = x.enumerate_components()
assert(y==[x[0]])
assert(y[0].transcript.parent==x.get_species())
def test_update_species(self):
from biocrnpyler import CombinatorialPromoter, Protein, Species, Combinatorial_Cooperative_Binding, \
DNAassembly,Transcription_MM, Translation_MM, Multimer, ComplexSpecies
#make a complicated promoter
newprom = CombinatorialPromoter("testprom",["treg1",Species("treg2",material_type="rna")],\
tx_capable_list = [["treg1","treg2"]],cooperativity={"testprom_treg2":1},leak=True)
newdna = DNAassembly("testDNA", promoter=newprom)
newdna.update_mechanisms(mechanisms={
"transcription": Transcription_MM(),
"translation": Translation_MM()
})
newdna.update_parameters(
parameters={
"cooperativity": 2,
"kb": 100,
"ku": 10,
"ktx": .05,
"ktl": .2,
"kdeg": 2
})
newprom_spec = newprom.update_species()
sp_treg1 = Species("treg1", material_type="protein")
sp_treg2 = Species("treg2", material_type="rna")
#mu_treg2 = Multimer(sp_treg2,2)
sp_dna = Species("testDNA", material_type="dna")
sp_rnap = Species("RNAP", material_type="protein")
sp_rna = Species("testDNA", material_type="rna")
cp_dna_rnap = ComplexSpecies([sp_dna, sp_rnap])
cp_dna_treg1 = ComplexSpecies([sp_dna, sp_treg1, sp_treg1])
cp_dna_treg2 = ComplexSpecies([sp_dna, sp_treg2])
cp_dna_treg1_rnap = ComplexSpecies([cp_dna_treg1, sp_rnap])
cp_dna_treg2_rnap = ComplexSpecies([cp_dna_treg2, sp_rnap])
cp_dna_treg1_treg2 = ComplexSpecies(
[sp_dna, sp_treg1, sp_treg1, sp_treg2])
cp_dna_treg1_treg2_rnap = ComplexSpecies([cp_dna_treg1_treg2, sp_rnap])
knownspecies = [sp_dna,sp_rnap,sp_rna,cp_dna_rnap,cp_dna_treg1,\
cp_dna_treg2,cp_dna_treg1_treg2,cp_dna_treg1_rnap, \
cp_dna_treg2_rnap,cp_dna_treg1_treg2_rnap]
#these are the species that should come out
test_set = set([str(a) for a in newprom_spec])
mistake_found = False
#we should have the correct length of species
self.assertTrue(len(test_set) == len(knownspecies))
for known_spec in knownspecies:
#go through and check each species if it's in the set generated by the promoter
if (str(known_spec) not in test_set):
print("couldn't find " + str(known_spec))
mistake_found = True
break
self.assertTrue(not mistake_found)
def test_update_mechanisms(self):
tx = Transcription_MM()
tl = Translation_MM()
deg = Degredation_mRNA_MM()
test_mech = {tx.mechanism_type: tx, tl.mechanism_type: tl}
default_test_mech = {deg.mechanism_type: deg}
# test that component has no mechanism
self.assertTrue(
isinstance(self.component.mechanisms, dict)
and len(self.component.mechanisms) == 0)
self.component.update_mechanisms(mixture_mechanisms=test_mech)
# test that the test_mech is registered as the only mechanism
self.assertEqual(self.component.mechanisms, test_mech)
self.component.default_mechanisms = default_test_mech
self.component.update_mechanisms(mixture_mechanisms=test_mech)
test_mech.update(default_test_mech)
self.assertEqual(self.component.mechanisms, test_mech)
# testing that the custom mechanism gets updated
self.assertTrue(
isinstance(self.component.custom_mechanisms, dict)
and len(self.component.custom_mechanisms) == 0)
self.component.update_mechanisms(mechanisms=test_mech)
self.assertEqual(self.component.custom_mechanisms, test_mech)
# testing that custom mechanism is protected by the overwrite_custom_mechanisms=False flag
self.component.update_mechanisms(mechanisms=default_test_mech,
overwrite_custom_mechanisms=False)
self.assertEqual(self.component.custom_mechanisms, test_mech)
# multiple mechanisms can be supplied with a list
test_mech_list = list(test_mech.values())
self.component.update_mechanisms(mechanisms=test_mech_list)
self.assertEqual(self.component.custom_mechanisms, test_mech)
# testing an invalid mechanism format
with self.assertRaisesRegexp(
ValueError,
'Mechanisms must be passed as a list of instantiated objects or a '
'dictionary {mechanism_type:mechanism instance}'):
self.component.update_mechanisms(mechanisms=(tx, tl))
def test_basic_RNAconstruct():
R = RBS("rbs")
C = CDS("gfp")
parameters={"cooperativity":2,"kb":100, "ku":10, "ktx":.05, "ktl":.2, "kdeg":2,"kint":.05}
mechs = {"translation":Translation_MM(Species("Ribo"))}
#minimal RNA translation
x = RNA_construct([R],mechanisms = mechs,parameters=parameters)
y = x.enumerate_components()
assert(not (R in y)) #RBS is copied correctly
assert([x[0]] == y) #RBS with no protein is still active
assert(y[0].protein is None) #protein is nothing
x = RNA_construct([[R,"reverse"]],mechanisms = mechs,parameters=parameters)
y = x.enumerate_components()
assert(y == []) #reverse RBS is not an RBS
assert(x[0].protein is None) #protein is nothing
#just a cds
x = RNA_construct([C],mechanisms = mechs,parameters=parameters)
y = x.enumerate_components()
assert(y==[]) #just a CDS does nothing
def test_update_reactions(self):
"""this function tests the CombinatorialPromoter for the ability to make
reactions with the proper inputs and outputs."""
from biocrnpyler import CombinatorialPromoter, Protein, Species, Combinatorial_Cooperative_Binding, \
DNAassembly,Transcription_MM, Translation_MM, Complex, ParameterKey
#make a relatively simple combinatorial promoter
parameters={"cooperativity":2,"kb":100, "ku":10, "ktx":.05,
ParameterKey(mechanism = None, part_id = "testprom_leak", name = "ktx"):.01,
ParameterKey(mechanism = None, part_id = "testprom_leak", name = "ku"):50,
ParameterKey(mechanism = None, part_id = "testprom_treg1_treg2_RNAP", name = "ku"):5}
newprom = CombinatorialPromoter("testprom",["treg1","treg2"],tx_capable_list=[["treg2","treg1"]], leak = True, parameters = parameters)
#you have to put it into an assembly
newdna = DNAassembly("testDNA",promoter=newprom)
#adding mechanisms because there is no mixture. I believe this is what the mixture does
sp_rnap = Species("RNAP",material_type="protein")
ribosome = Species("Ribo", material_type = "protein")
newdna.add_mechanisms({"transcription":Transcription_MM(rnap = sp_rnap), "translation":Translation_MM(ribosome = ribosome)})
#you have to do update_species first
newprom_copy = newdna.promoter #Promoters are copied when added to DNAassemblies
newprom_spec = newprom_copy.update_species()
#now the test... does it produce the right reactions??
newprom_rxns = newprom_copy.update_reactions()
#here i am generating the species manually
sp_dna = Species("testDNA",material_type="dna")
sp_rna = Species("testDNA",material_type="rna")
sp_treg1 = Species("treg1",material_type="protein")
sp_treg2 = Species("treg2",material_type="protein")
#now the complexes
sp_dna_treg1 = Complex([sp_dna,sp_treg1,sp_treg1])
sp_dna_treg2 = Complex([sp_dna,sp_treg2,sp_treg2])
sp_dna_treg1_treg2 = Complex([sp_dna,sp_treg2,sp_treg2,sp_treg1,sp_treg1])
sp_dna_rnap = Complex([sp_dna,sp_rnap])
sp_dna_treg1_rnap = Complex([sp_dna_treg1,sp_rnap])
sp_dna_treg2_rnap = Complex([sp_dna_treg2,sp_rnap])
sp_dna_treg1_treg2_rnap = Complex([sp_dna_treg1_treg2,sp_rnap])
#print('\n\n'.join([str(a) for a in newprom_rxns]))
#now, we generate the reaction input outputs manually
r0 = [set([sp_rnap,sp_dna]),set([sp_dna_rnap]),100,50] #RNAP binding to DNA
r1 = [set([sp_dna_rnap]),set([sp_dna,sp_rna,sp_rnap]),.01,None] #leaky transcription
r2 = [set([sp_dna,sp_treg1]),set([sp_dna_treg1]),100,10] #treg1 binding
r3 = [set([sp_dna_treg1,sp_rnap]),set([sp_dna_treg1_rnap]),100,50] #rnap binding to treg1 bound dna
r4 = [set([sp_dna_treg1_rnap]),set([sp_dna_treg1,sp_rnap,sp_rna]),.01,None] #leaky tx from single regulator
r5 = [set([sp_dna_treg2_rnap]),set([sp_dna_treg2,sp_rnap,sp_rna]),.01,None] #leaky tx from single regulator
r6 = [set([sp_dna_treg1_treg2_rnap]),set([sp_dna_treg1_treg2,sp_rnap,sp_rna]),.05,None] #ktx for regular tx
r7 = [set([sp_dna_treg2,sp_rnap]),set([sp_dna_treg2_rnap]),100,50] #rnap binding to treg2 bound dna
r8 = [set([sp_dna,sp_treg2]),set([sp_dna_treg2]),100,10] #treg2 binding
r9 = [set([sp_dna_treg1,sp_treg2]),set([sp_dna_treg1_treg2]),100,10] #treg2 binding to dna that already has treg1
r10 = [set([sp_dna_treg2,sp_treg1]),set([sp_dna_treg1_treg2]),100,10] #treg1 binding to dna that already has treg2
r11 = [set([sp_dna_treg1_treg2,sp_rnap]),set([sp_dna_treg1_treg2_rnap]),100,5] #rnap binding to full complex
truthlist = [r0,r1,r2,r3,r4,r5,r6,r7,r8,r9,r10,r11]
#print('\n\n'.join([str(a) for a in newprom_rxns]))
for rxn in newprom_rxns:
in_outs = [set([i.species for i in rxn.inputs]), set([o.species for o in rxn.outputs])]
correctPick = False
for rset in truthlist:
#go through all the reactions and make sure that
#they have the correct inputs, outputs, and constants.
if(rset[0]==in_outs[0] and rset[1] == in_outs[1]):
self.assertTrue(rxn.propensity_type.k_forward == rset[2])
self.assertTrue(rxn.propensity_type.k_reverse == rset[3])
correctPick = True
break
self.assertTrue(correctPick)
#12 reactions must be generated
self.assertTrue(len(newprom_rxns)==len(truthlist))
#then we should also test what happens if you say that nothing can transcribe:
newprom2 = CombinatorialPromoter("testprom",["treg1"], parameters = parameters,tx_capable_list = [],leak=False,\
mechanisms={"transcription":Transcription_MM(rnap = sp_rnap), "translation":Translation_MM(ribosome = ribosome)})
newdna2 = DNAassembly("testDNA",promoter=newprom2)
#adding mechanisms because there is no mixture. I believe this is what the mixture does
sp_rnap = Species("RNAP",material_type="protein")
ribosome = Species("Ribo", material_type = "protein")
self.assertWarnsRegex(UserWarning, 'nothing can transcribe',newdna2.update_reactions)
def test_update_species(self):
from biocrnpyler import CombinatorialPromoter, Protein, Species, Combinatorial_Cooperative_Binding, \
DNAassembly,Transcription_MM, Translation_MM, Complex
#make a complicated promoter
newprom = CombinatorialPromoter("testprom",["treg1",Species("treg2",material_type="rna")],\
tx_capable_list = [["treg1","treg2"]],cooperativity={"testprom_treg2":1},leak=True)
sp_rnap = Species("RNAP",material_type="protein")
ribosome = Species("Ribo", material_type = "protein")
newdna = DNAassembly("testDNA",promoter=newprom)
newdna.add_mechanisms({"transcription":Transcription_MM(rnap = sp_rnap), "translation":Translation_MM(ribosome = ribosome)})
newdna.update_parameters(parameters={"cooperativity":2,"kb":100, "ku":10, "ktx":.05, "ktl":.2, "kdeg":2})
#Promoters are copied when added to DNAassemblies
newprom_copy = newdna.promoter
newprom_spec = newprom_copy.update_species()
sp_treg1 = Species("treg1",material_type="protein")
sp_treg2 = Species("treg2",material_type="rna")
sp_dna = Species("testDNA",material_type="dna")
sp_rna = Species("testDNA",material_type="rna")
cp_dna_rnap = Complex([sp_dna,sp_rnap])
cp_dna_treg1 = Complex([sp_dna,sp_treg1,sp_treg1])
cp_dna_treg2 = Complex([sp_dna,sp_treg2])
cp_dna_treg1_rnap = Complex([cp_dna_treg1,sp_rnap])
cp_dna_treg2_rnap = Complex([cp_dna_treg2,sp_rnap])
cp_dna_treg1_treg2 = Complex([sp_dna,sp_treg1,sp_treg1,sp_treg2])
cp_dna_treg1_treg2_rnap = Complex([cp_dna_treg1_treg2,sp_rnap])
knownspecies = [sp_dna,sp_rnap,sp_rna,cp_dna_rnap,cp_dna_treg1,\
cp_dna_treg2,cp_dna_treg1_treg2,cp_dna_treg1_rnap, \
cp_dna_treg2_rnap,cp_dna_treg1_treg2_rnap,sp_treg1,sp_treg2]
#these are the species that should come out
test_set = set([str(a) for a in newprom_spec])
mistake_found = False
error_txt = ""
for known_spec in knownspecies:
#go through and check each species if it's in the set generated by the promoter
if(str(known_spec) not in test_set):
error_txt += "\ncouldn't find "+str(known_spec)
mistake_found = True
if mistake_found:
raise ValueError(f"Mistake found in Species output:{error_txt}. Returned Species: {test_set}.")
#we should have the correct length of species
self.assertTrue(len(test_set)==len(knownspecies))
self.assertTrue(not mistake_found)
def test_update_reactions(self):
"""this function tests the CombinatorialPromoter for the ability to make
reactions with the proper inputs and outputs."""
from biocrnpyler import CombinatorialPromoter, Protein, Species, Combinatorial_Cooperative_Binding, \
DNAassembly,Transcription_MM, Translation_MM, ComplexSpecies, Multimer
#make a relatively simple combinatorial promoter
newprom = CombinatorialPromoter("testprom", ["treg1", "treg2"],
tx_capable_list=[["treg2", "treg1"]],
leak=True)
#you have to put it into an assembly
newdna = DNAassembly("testDNA", promoter=newprom)
#adding mechanisms because there is no mixture. I believe this is what the mixture does
newdna.update_mechanisms(mechanisms={
"transcription": Transcription_MM(),
"translation": Translation_MM()
})
newdna.update_parameters(parameters={"cooperativity":2,"kb":100, "ku":10, "ktx":.05, ("testprom_leak","ktx"):.01,\
("testprom_leak","ku"):50,("testprom_treg1_treg2_RNAP","ku"):5})
#you have to do update_species first
newprom_spec = newprom.update_species()
#now the test... does it produce the right reactions??
newprom_rxns = newprom.update_reactions()
#here i am generating the species manually
sp_dna = Species("testDNA", material_type="dna")
sp_rna = Species("testDNA", material_type="rna")
sp_treg1 = Species("treg1", material_type="protein")
sp_treg2 = Species("treg2", material_type="protein")
sp_rnap = Species("RNAP", material_type="protein")
#now the complexes
sp_dna_treg1 = ComplexSpecies([sp_dna, sp_treg1, sp_treg1])
sp_dna_treg2 = ComplexSpecies([sp_dna, sp_treg2, sp_treg2])
sp_dna_treg1_treg2 = ComplexSpecies(
[sp_dna, sp_treg2, sp_treg2, sp_treg1, sp_treg1])
sp_dna_rnap = ComplexSpecies([sp_dna, sp_rnap])
sp_dna_treg1_rnap = ComplexSpecies([sp_dna_treg1, sp_rnap])
sp_dna_treg2_rnap = ComplexSpecies([sp_dna_treg2, sp_rnap])
sp_dna_treg1_treg2_rnap = ComplexSpecies([sp_dna_treg1_treg2, sp_rnap])
#print('\n\n'.join([str(a) for a in newprom_rxns]))
#now, we generate the reaction input outputs manually
r0 = [set([sp_rnap, sp_dna]),
set([sp_dna_rnap]), 100, 50] #RNAP binding to DNA
r1 = [set([sp_dna_rnap]),
set([sp_dna, sp_rna, sp_rnap]), .01, 0] #leaky transcription
r2 = [set([sp_dna, sp_treg1]),
set([sp_dna_treg1]), 100, 10] #treg1 binding
r3 = [set([sp_dna_treg1, sp_rnap]),
set([sp_dna_treg1_rnap]), 100,
50] #rnap binding to treg1 bound dna
r4 = [
set([sp_dna_treg1_rnap]),
set([sp_dna_treg1, sp_rnap, sp_rna]), .01, 0
] #leaky tx from single regulator
r5 = [
set([sp_dna_treg2_rnap]),
set([sp_dna_treg2, sp_rnap, sp_rna]), .01, 0
] #leaky tx from single regulator
r6 = [
set([sp_dna_treg1_treg2_rnap]),
set([sp_dna_treg1_treg2, sp_rnap, sp_rna]), .05, 0
] #ktx for regular tx
r7 = [set([sp_dna_treg2, sp_rnap]),
set([sp_dna_treg2_rnap]), 100,
50] #rnap binding to treg2 bound dna
r8 = [set([sp_dna, sp_treg2]),
set([sp_dna_treg2]), 100, 10] #treg2 binding
r9 = [
set([sp_dna_treg1, sp_treg2]),
set([sp_dna_treg1_treg2]), 100, 10
] #treg2 binding to dna that already has treg1
r10 = [
set([sp_dna_treg2, sp_treg1]),
set([sp_dna_treg1_treg2]), 100, 10
] #treg1 binding to dna that already has treg2
r11 = [
set([sp_dna_treg1_treg2, sp_rnap]),
set([sp_dna_treg1_treg2_rnap]), 100, 5
] #rnap binding to full complex
truthlist = [r0, r1, r2, r3, r4, r5, r6, r7, r8, r9, r10, r11]
#print('\n\n'.join([str(a) for a in newprom_rxns]))
for rxn in newprom_rxns:
in_outs = [set(rxn.inputs), set(rxn.outputs)]
correctPick = False
for rset in truthlist:
#go through all the reactions and make sure that
#they have the correct inputs, outputs, and constants.
if (rset[0] == in_outs[0] and rset[1] == in_outs[1]):
self.assertTrue(rxn.k == rset[2])
self.assertTrue(rxn.k_r == rset[3])
correctPick = True
break
self.assertTrue(correctPick)
#12 reactions must be generated
self.assertTrue(len(newprom_rxns) == len(truthlist))
#TODO: tests below this are questionable
#then we should also test what happens if you say that nothing can transcribe:
newprom2 = CombinatorialPromoter("testprom",
["treg1"]) #,tx_capable_list = [])
newdna2 = DNAassembly("testDNA", promoter=newprom2)
#adding mechanisms because there is no mixture. I believe this is what the mixture does
newdna2.update_mechanisms(mechanisms={
"transcription": Transcription_MM(),
"translation": Translation_MM()
})
newdna2.update_parameters(parameters={
"cooperativity": 2,
"kb": 100,
"ku": 10,
"ktx": .05
})
with self.assertWarns(UserWarning):
#TODO fix this with a warning detection system that actually checks for the proper warning
newprom_rxns = newprom2.update_reactions()
def test_combinatorial_DNAconstruct_RNAconstruct():
P = Promoter("pconst") #constitutive promoter
U = RBS("rbs")
C = CDS("gfp")
T = Terminator("term")
correct_order_list = [P, U, C, T]
directions_list = ["forward", "reverse"]
index_list = range(4)
parameters = {
"cooperativity": 2,
"kb": 100,
"ku": 10,
"ktx": .05,
"ktl": .2,
"kdeg": 2,
"kint": .05
}
mechs = {
"transcription":
Transcription_MM(Species("RNAP", material_type="protein")),
"translation": Translation_MM(Species("Ribo"))
}
iter_list = []
for order in permutations(correct_order_list):
for i in range(4):
for direction in directions_list:
new_order = list(order)
new_order[i] = [order[i], direction]
iter_list += [new_order]
try:
for combination in iter_list:
x = DNA_construct(combination,
mechanisms=mechs,
parameters=parameters)
print(x)
y = x.enumerate_components()
z = []
#promoter at the beginning facing reverse doesn't make a transcript
if ((isinstance(x[0], Promoter) and x[0].direction == "reverse")):
assert (y == [x[0]])
#promoter at the end facing forward doesn't make a transcript
elif ((isinstance(x[-1], Promoter)
and x[-1].direction == "forward")):
assert (y == [x[-1]])
#everything else should make one transcript
else:
assert (isinstance(y[1], RNA_construct))
for element in y:
#find the RNA
if (isinstance(element, RNA_construct)):
rna_enumeration = element.enumerate_components()
#reverse RBS does not function in RNA
if any([
p.direction == 'reverse' for p in element
if isinstance(p, RBS)
]):
assert (len(rna_enumeration) == 0)
elif (U in element):
#if there is an RBS and it is not reverse, then it should be active
assert (len(rna_enumeration) >= 1)
else:
#if there is no RBS in the RNA then the RNA cannot do anything
assert (len(rna_enumeration) == 0)
if (len(rna_enumeration) == 2):
#if two things are returned, that means that a protein is made, and
#this is only possible if there is an RBS and CDS in the forward
#orientation
assert (any([
p.direction == 'forward' for p in element
if isinstance(p, RBS)
]))
assert (any([
p.direction == 'forward' for p in element
if isinstance(p, CDS)
]))
except Exception as e:
error_txt = f"Combinatorial enumerate_components failed when parts list was {combination}. \n Unexpected Error: {str(e)}"
raise Exception(error_txt)