def test_promoter_from_promoter():
test_name = 'test_promoter'
test_length = 10
prom = Promoter(name=test_name, length=test_length)
assert prom.assembly is None
assert prom.transcript is None
assert prom.protein is None
test_assembly = 'test_assembly'
test_transcript = 'test_transcript'
test_protein = 'test_protein'
prom2 = Promoter.from_promoter(name=prom,
assembly=test_assembly,
transcript=test_transcript,
protein=test_protein)
assert prom2.assembly == test_assembly
assert prom2.transcript == test_transcript
assert prom2.protein == test_protein
# check that original values are kept
assert prom2.name == test_name
assert prom2.length == test_length
with pytest.raises(
TypeError,
match='Promoter can be initialized from string or another promoter!'
):
Promoter.from_promoter(name=Species(name=test_name),
assembly=test_assembly,
transcript=test_transcript,
protein=test_protein)
def test_promoter_DNAconstruct():
P = Promoter("pconst") #constitutive promoter
parameters = {
"cooperativity": 2,
"kb": 100,
"ku": 10,
"ktx": .05,
"ktl": .2,
"kdeg": 2,
"kint": .05
}
mechs = {
"transcription":
Transcription_MM(Species("RNAP", material_type="protein"))
}
x = DNA_construct([P], mechanisms=mechs, parameters=parameters)
assert (not (P in x.parts_list)) #make sure P is copied
assert (P in x) #testing "contains" function of Construct
y = x.enumerate_components()
assert ([x[0]] == y)
assert (x[0].transcript is None)
#works in reverse as well
x = DNA_construct([[P, "reverse"]],
mechanisms=mechs,
parameters=parameters)
assert (not (P in x.parts_list)) #make sure P is copied
assert (P in x) #testing "contains" function of Construct
y = x.enumerate_components()
assert ([x[0]] == y)
assert (x[0].transcript is None)
def test_update_promoter():
T = Species("T")
D = Species("D")
P = Species("P")
prom = Promoter("prom")
mech = Mechanism(name="mech", mechanism_type="assembly")
ass = DNAassembly("ass",
rbs=None,
promoter=None,
transcript=T,
dna=D,
protein=P,
mechanisms=[mech])
ass.update_promoter(prom)
#test copying
assert ass.promoter != prom
assert type(ass.promoter) == type(prom)
assert ass.promoter.name == prom.name
#test resetting transcript
assert ass.promoter.transcript == T
#test mechanism inheritance
assert mech.mechanism_type in ass.promoter.mechanisms
def test_add_mechanism():
mech = Mechanism(name="mech", mechanism_type="assembly")
ass = DNAassembly(name="ass", rbs="rbs", promoter="prom")
ass.add_mechanism(mech)
#Mechanism should be added to promoter and rbs
assert mech.mechanism_type in ass.mechanisms
assert mech.mechanism_type in ass.promoter.mechanisms
assert mech.mechanism_type in ass.rbs.mechanisms
#Mechaisms which are already in the Promoter or RBS should NOT be overwritten
mech_rbs = Mechanism(name="rbs", mechanism_type="mech")
mech_promoter = Mechanism(name="promoter", mechanism_type="mech")
mech_assembly = Mechanism(name="assembly", mechanism_type="mech")
#Create promoter and assembly with their own mechanisms
prom = Promoter("prom", mechanisms=[mech_promoter])
assert mech_promoter.mechanism_type in prom.mechanisms
rbs = RBS("rbs", mechanisms=[mech_rbs])
assert mech_rbs.mechanism_type in rbs.mechanisms
ass = DNAassembly(name="ass", rbs=rbs, promoter=prom)
assert ass.rbs.mechanisms["mech"].name == mech_rbs.name
assert ass.promoter.mechanisms["mech"].name == mech_promoter.name
#Overwrite the assembly mechanism
#this should not propogate down to rbs or promoter!
ass.add_mechanism(mech_assembly)
assert mech_assembly.mechanism_type in ass.mechanisms
assert ass.rbs.mechanisms["mech"].name == mech_rbs.name
assert ass.promoter.mechanisms["mech"].name == mech_promoter.name
def test_dictionary_search():
colordict = {"p1":"blue","Promoter":"red","Bxb1":"orange",\
("Bxb1","attP"):"mauve","attP":"green",\
"protein":"purple",("phosphorylated",):"yellow"}
prom = Promoter("p1")
prom2 = Promoter("p2")
c1 = CDS("ooga")
prot = Species("myprot", material_type="protein")
rna1 = Species("myrna", material_type="rna")
rna1.add_attribute("phosphorylated")
prot2 = Species("myprot2", material_type="protein")
prot2.add_attribute("phosphorylated")
int1 = Species("Bxb1", "protein")
int2 = IntegraseSite("attP", "attP", "Int1")
int3 = IntegraseSite("attP", "attP", "Bxb1")
int4 = IntegraseSite("attP2", "attP", "Bxb1")
int5 = IntegraseSite("attP3e", "attP")
print(int4.name)
print(repr(int4))
print((int4.integrase, int4.site_type))
assert (member_dictionary_search(prom,
colordict) == "blue") #DNA_part name
assert (member_dictionary_search(prom2,
colordict) == "red") #DNA_part type
assert (member_dictionary_search(c1, colordict) == None
) #this one is not found
assert (member_dictionary_search(prot,
colordict) == "purple") #material type
assert (member_dictionary_search(rna1, colordict) == "yellow"
) #attribute is colored
assert (member_dictionary_search(prot2, colordict) == "purple"
) #attribute is colored
colordict[("protein", ("phosphorylated", ))] = "darkblue"
assert (member_dictionary_search(prot2, colordict) == "darkblue"
) #(material_type,attribute) is colored differntly
assert (member_dictionary_search(int1, colordict) == "orange"
) #integrase protein is colored
assert (member_dictionary_search(int5, colordict) == "green"
) #site type in the dictionary
assert (
member_dictionary_search(int3, colordict) == "green"
) #name of attP is more important than tuple of integrase, attP type
assert (member_dictionary_search(int4, colordict) == "mauve"
) #now integrase and type are supreme, since name doesn't match
def test_combinatorial_enumeration_DNAconstruct():
P = Promoter("pconst") #constitutive promoter
T = Terminator("term")
parameters = {
"cooperativity": 2,
"kb": 100,
"ku": 10,
"ktx": .05,
"ktl": .2,
"kdeg": 2,
"kint": .05
}
mechs = {
"transcription":
Transcription_MM(Species("RNAP", material_type="protein"))
}
#circular construct
x = DNA_construct([P, P, T],
mechanisms=mechs,
parameters=parameters,
circular=True)
y = x.combinatorial_enumeration()
prom_positions = []
dna_species = {}
for prom_comp in y:
if (prom_comp.position not in dna_species):
dna_species[prom_comp.position] = [prom_comp.dna_to_bind.parent]
else:
dna_species[prom_comp.position] += [prom_comp.dna_to_bind.parent]
p1_bound = Complex(
[x.get_species()[0],
Species("RNAP", material_type="protein")]).parent
p2_bound = Complex(
[x.get_species()[1],
Species("RNAP", material_type="protein")]).parent
both_bound = Complex(
[p1_bound[1], Species("RNAP", material_type="protein")]).parent
assert (x.get_species() in dna_species[0]
) #unbound polymer found in combinatorial enumeration
assert (p2_bound in dna_species[0]
) #proper bound polymer found in combinatorial enumeration
assert (x.get_species() in dna_species[1]
) #unbound polymer found in combinatorial enumeration
assert (p1_bound in dna_species[1]
) #proper bound polymer found in combinatorial enumeration
assert (
both_bound not in dna_species[0]
) #dna with both promoters bound is not in combinatorial enumeration
assert (
both_bound not in dna_species[1]
) #dna with both promoters bound is not in combinatorial enumeration
assert (len(y) == 4)
def test_promoter_terminator_DNAconstruct():
P = Promoter("pconst") #constitutive promoter
T = Terminator("term")
parameters = {
"cooperativity": 2,
"kb": 100,
"ku": 10,
"ktx": .05,
"ktl": .2,
"kdeg": 2,
"kint": .05
}
mechs = {
"transcription":
Transcription_MM(Species("RNAP", material_type="protein"))
}
#minimal RNA transcription
x = DNA_construct([P, T], mechanisms=mechs, parameters=parameters)
y = x.enumerate_components()
assert (y[0] == x[0]) #correct promoter is returned
assert (
x[0].transcript == y[1].get_species()
) #promoter in the DNA_construct has the correct transcript species
assert (y[1].promoter == x[0]
) #rna is linked back to the DNA_construct's promoter
assert (y[1].promoter == y[0]
) #correct promoter is returned by enumerate_constructs
#"incoherent" transcription
x = DNA_construct([[P, "reverse"], T],
mechanisms=mechs,
parameters=parameters)
y = x.enumerate_components()
assert (y == [x[0]]) #correct promoter is returned
#transcription in reverse works as well
x = DNA_construct([T, [P, "reverse"]],
mechanisms=mechs,
parameters=parameters)
y = x.enumerate_components()
assert (y[0] == x[1]) #correct promoter is returned
assert (
x[1].transcript == y[1].get_species()
) #promoter in the DNA_construct has the correct transcript species
assert (y[1].promoter == x[1]
) #rna is linked back to the DNA_construct's promoter
assert (y[1].promoter == y[0]
) #correct promoter is returned by enumerate_constructs
def test_get_part_DNAconstruct():
P = Promoter("pconst")
U = RBS("utr1")
C = CDS("coolprot1")
T = Terminator("T11")
T2 = Terminator("iamsoterminator")
parameters = {
"cooperativity": 2,
"kb": 100,
"ku": 10,
"ktx": .05,
"ktl": .2,
"kdeg": 2,
"kint": .05
}
mechs = {
"transcription":
Transcription_MM(Species("RNAP", material_type="protein"))
}
x = DNA_construct([P, U, C, T, T2],
mechanisms=mechs,
parameters=parameters)
with pytest.raises(
ValueError,
match=
r"get_component requires a single keyword. Recieved component=None, name=None, index=None."
):
y = x.get_part()
with pytest.raises(ValueError):
y = x.get_part(part=P, index=3)
with pytest.raises(ValueError):
y = x.get_part(part="oogabooga")
with pytest.raises(ValueError):
y = x.get_part(part_type="oogabooga")
with pytest.raises(ValueError):
y = x.get_part(name=5)
with pytest.raises(ValueError):
y = x.get_part(index="oogabooga")
assert (x.get_part(part_type=Promoter) == x[0])
assert (x.get_part(name="pconst") == x[0])
assert (x.get_part(index=2) == x[2])
assert (x.get_part(part=P) == x[0])
assert (len(x.get_part(part_type=Terminator)) == 2)
def test_polymer_transformation():
prom = Promoter("p1")
utr = RBS("utr")
cds = CDS("GFP")
cds2 = CDS("RFP")
term = Terminator("t16")
construct = DNA_construct([prom, utr, cds, term])
construct2 = DNA_construct([cds2])
dummy = Polymer_transformation.dummify(construct, "input1")
assert (dummy.name == "input1") #dummy polymer has the right name
assert (len(dummy.polymer) == len(construct)
) #dummy polymer has the right length
assert ([a.direction for a in dummy] == [a.direction for a in construct]
) #dummy polymer monomers have the right direction
assert ([a.position for a in dummy] == [a.position for a in construct]
) #dummy polymer monomers have the right position
assert (isinstance(dummy, NamedPolymer)
) #make sure the output of dummify has the right type
assert (isinstance(dummy, OrderedPolymer)
) #make sure the output of dummify has the right type
dummy2 = Polymer_transformation.dummify(construct, "input2")
transformation = Polymer_transformation(
[dummy[0], [prom, "forward"], dummy2[0]], circular=True)
assert (transformation.circular == True
) #make sure circular is set properly
assert (len(transformation.parentsdict) == 2) #two parents!
assert (transformation.create_polymer(
[construct, construct2]) == DNA_construct([prom, prom, cds2],
circular=True)
) #transformations are performed correctly
assert (transformation.create_polymer(
[construct2, construct]) == DNA_construct([cds2, prom, prom],
circular=True))
assert ("(input1-0)(p1)(input2-0)"
in str(transformation)) #contains vital information in the repr
def test_integrase_rule():
prom = Promoter("p1")
utr = RBS("utr")
cds = CDS("GFP")
cds2 = CDS("RFP")
term = Terminator("t16")
ap = IntegraseSite("attP", "attP")
ab = IntegraseSite("attB", "attB")
aflp = IntegraseSite("FLP", "FLP")
delete = DNA_construct([ab, cds, ap])
flip = DNA_construct([ab, cds, [ap, "reverse"]])
plasp = DNA_construct([cds, ap], circular=True)
plasb = DNA_construct([cds, ab], circular=True)
genp = DNA_construct([cds2, ap])
genb = DNA_construct([cds2, ab])
bxb1_rule = IntegraseRule(name="Bxb1",
reactions={
("attB", "attP"): "attL",
("attP", "attB"): "attR"
})
assert (set(["attP", "attB", "attL", "attR"]) == set(bxb1_rule.attsites))
assert (set(["attP", "attB", "attL", "attR"]) == set(bxb1_rule.binds_to()))
assert (bxb1_rule.integrase_species == Species("Bxb1",
material_type="protein"))
bxb1_enumerator = Integrase_Enumerator("Bxb1",
int_mechanisms={"Bxb1": bxb1_rule})
flp_rule = IntegraseRule(name="FLP", reactions={("FLP", "FLP"): "FLP"})
bad_rule = IntegraseRule(name="Bxb1", reactions={("attB", "attP"): "attL"})
with pytest.raises(AssertionError):
bxb1_rule.generate_products(delete[0],
delete[2]) #must have the right integrase
delete[0].update_integrase("Bxb1")
delete[2].update_integrase("Bxb1")
with pytest.raises(KeyError):
bxb1_rule.generate_products(delete[0],
delete[0]) #attP+attP is not possible
with pytest.raises(KeyError):
bad_rule.generate_products(
delete[0],
delete[2]) #attP->attB reaction is not possible with a bad rule
aL = IntegraseSite("attL", "attL", integrase="Bxb1")
aL.direction = "forward"
aR = IntegraseSite("attR", "attR", integrase="Bxb1")
aR.direction = "forward"
productsites = bxb1_rule.generate_products(delete[0], delete[2])
testaL = copy.copy(aL)
testaL.direction = "forward"
testaL.position = 0
testaL.parent = delete
testaR = copy.copy(aR)
testaR.direction = "forward"
testaR.position = 2
testaR.parent = delete
assert (
productsites[0] == testaL
) #generated product sites have the right parent, position, and direction
assert (
productsites[1] == testaR
) #generated product sites have the right parent, position, and direction
ap = IntegraseSite("attP", "attP", integrase="Bxb1")
ab = IntegraseSite("attB", "attB", integrase="Bxb1")
delete = DNA_construct([ab, cds, ap])
flip = DNA_construct([ab, cds, [ap, "reverse"]], circular=True)
flipr = flip.get_reversed()
plasp = DNA_construct([cds, ap], circular=True)
plasb = DNA_construct([cds, ab], circular=True)
genp = DNA_construct([cds2, ap])
genb = DNA_construct([cds2, ab])
#testing the actual integration reactions
#inversion
new_constructs = bxb1_rule.integrate(flip[0], flip[2],
also_inter=False) #sites forwards
assert (len(new_constructs) == 1) #one product is made
assert ([part.name
for part in new_constructs[0]] == ["attL", "GFP", "attR"])
assert ([part.direction for part in new_constructs[0]
] == ["forward", "reverse", "reverse"])
new_constructs = bxb1_rule.integrate(flip[2], flip[0],
also_inter=False) #sites reverse
assert (len(new_constructs) == 1) #one product is made
assert ([part.name
for part in new_constructs[0]] == ["attL", "GFP", "attR"])
assert ([part.direction for part in new_constructs[0]
] == ["forward", "reverse", "reverse"])
new_constructs = bxb1_rule.integrate(flipr[2], flipr[0],
also_inter=False) #sites forwards
assert (len(new_constructs) == 1) #one product is made
assert ([part.name
for part in new_constructs[0]] == ["attR", "GFP", "attL"])
assert ([part.direction for part in new_constructs[0]
] == ["forward", "forward", "reverse"])
new_constructs = bxb1_rule.integrate(
flip[0], flip[2], also_inter=True) #allow intermolecular reactions
assert (len(new_constructs) == 2) #now, two products are made
assert (sum([a.circular
for a in new_constructs]) == 2) #all of them is circular
for prod in new_constructs:
if (len(prod) == 3):
assert ([part.name for part in prod] == ["attL", "GFP", "attR"])
assert ([part.direction
for part in prod] == ["forward", "reverse", "reverse"])
else:
assert ([part.name for part in prod
] == ['attL', 'GFP', 'attB', 'attR', 'GFP', 'attP'])
assert ([part.direction for part in prod] == [
"forward", "reverse", "reverse", "forward", "forward",
"reverse"
])
#deletion
new_constructs = bxb1_rule.integrate(delete[0],
delete[2],
also_inter=False) #sites forwards
assert (len(new_constructs) == 2) #two product is made
assert (sum([a.circular
for a in new_constructs]) == 1) #one of them is circular
for prod in new_constructs:
if (prod.circular):
assert ([part.name for part in prod] == ["attR", "GFP"])
assert ([part.direction
for part in prod] == ["forward", "forward"])
else:
assert ([part.name for part in prod] == ["attL"])
assert ([part.direction for part in prod] == ["forward"])
#now, what if we also calculate the intermolecular reactions?
new_constructs = bxb1_rule.integrate(delete[2], delete[0],
also_inter=True) #sites reverse
assert (len(new_constructs) == 3) #four product is made
assert (sum([a.circular
for a in new_constructs]) == 1) #one of them is circular
for prod in new_constructs:
if (prod.circular):
if (len(prod) == 2):
print(prod)
assert ([part.name for part in prod] == ["attR", "GFP"])
assert ([part.direction
for part in prod] == ["forward", "forward"])
elif (len(prod) == 1):
assert ([part.name for part in prod] == ["attL"])
assert ([part.direction for part in prod] == ["forward"])
elif (len(prod) == 5):
assert ([part.name for part in prod
] == ["attB", "GFP", "attR", "GFP", "attP"])
assert ([part.direction for part in prod] == ["forward"] * 5)
#integration
new_constructs = bxb1_rule.integrate(
plasp[1], plasb[1]) #two plasmids -> one plasmid p then b
assert (len(new_constructs) == 1) #one product is made
prod = new_constructs[0]
assert ([part.name for part in prod] == ["GFP", "attR", "GFP", "attL"])
assert ([part.direction
for part in prod] == ["forward", "forward", "forward", "forward"])
assert (new_constructs[0].circular)
new_constructs = bxb1_rule.integrate(
plasb[1], plasp[1]) #two plasmids -> one plasmid b then p
assert (len(new_constructs) == 1) #one product is made
prod = new_constructs[0]
assert ([part.name for part in prod] == ["GFP", "attL", "GFP", "attR"])
assert ([part.direction
for part in prod] == ["forward", "forward", "forward", "forward"])
assert (new_constructs[0].circular)
bxb1_enumerator.reset([plasb, plasp])
assert (len(plasb[1].linked_sites) == 0
) #linked sites are nonexistant if it is reset
assert (len(plasp[1].linked_sites) == 0
) #linked sites are nonexistant if it is reset
#include result construct
result_construct = DNA_construct([cds, aL, cds, aR], circular=True)
new_constructs = bxb1_rule.integrate(
plasb[1], plasp[1],
existing_dna_constructs=[result_construct
]) #two plasmids -> one plasmid b then p
assert (len(new_constructs) == 0
) #no new products are made, only the existing one
assert (
(plasp[1], True)
in plasb[1].linked_sites) #proper reaction found inside integrase site
assert (
(plasb[1], True)
in plasp[1].linked_sites) #proper reaction found inside integrase site
#including circularly permuted existing construct
#reaction is:
#[cds,ab] + [cds,ap] =[cds, aL, cds, aR]
bxb1_enumerator.reset([plasb, plasp])
permuted_construct = DNA_construct([cds, aR, cds, aL], circular=True)
new_constructs = bxb1_rule.integrate(
plasb[1], plasp[1],
existing_dna_constructs=[permuted_construct
]) #two plasmids -> one plasmid b then p
assert (len(new_constructs) == 0
) #no new products are made, only the existing one
assert (
(plasp[1], True)
in plasb[1].linked_sites) #proper reaction found inside integrase site
assert (
(plasb[1], True)
in plasp[1].linked_sites) #proper reaction found inside integrase site
bxb1_enumerator.reset([plasb, plasp])
new_constructs = bxb1_rule.integrate(genb[1],
plasp[1]) #linear with circular
assert (len(new_constructs) == 1) #one product is made
prod = new_constructs[0]
assert ([part.name for part in prod] == ['RFP', 'attL', 'GFP', 'attR'])
assert ([part.direction
for part in prod] == ["forward", "forward", "forward", "forward"])
assert (not new_constructs[0].circular)
#reverse integration
bxb1_enumerator.reset([plasb, plasp])
new_constructs = bxb1_rule.integrate(plasp[1],
genb[1]) #circular with linear
assert (len(new_constructs) == 1) #one product is made
prod = new_constructs[0]
assert ([part.name for part in prod] == ['RFP', 'attL', 'GFP', 'attR'])
assert ([part.direction
for part in prod] == ["forward", "forward", "forward", "forward"])
assert (not new_constructs[0].circular)
#recombination
bxb1_enumerator.reset([plasb, plasp])
new_constructs = bxb1_rule.integrate(genp[1], genb[1]) #linear with linear
assert (len(new_constructs) == 2) #two products
assert (sum([a.circular
for a in new_constructs]) == 0) #all products are linear
for prod in new_constructs:
assert ([part.name for part in prod] in [['RFP', 'attL'],
['RFP', 'attR']])
assert ([part.direction for part in prod] == ["forward", "forward"])
def test_compilation():
#Create an infinite polymer system and compile it at different recursion depths
pconst = Promoter("pconst") #constitutive promoter
gfp = CDS("GFP")
rfp = CDS("RFP")
t16 = Terminator("t16") #a terminator stops transcription
#some parameters are useful also. note the "kint" parameter which determines the rate of recombination
parameters = {
"cooperativity": 2,
"kb": 100,
"ku": 10,
"ktx": .05,
"ktl": .2,
"kdeg": 2,
"kint": .05
}
#here is where we define the integrase attachment sites
attP = IntegraseSite(
"attP", "attP", integrase="Bxb1"
) #the first argument is the name of this attachment site, the second argument is the type of attachment site it is ("attP", "attB", "attL" or "attR") and the integrase denotes which integrase binds to this site (default is "int1")
attB = IntegraseSite(
"attB", "attB", integrase="Bxb1"
) #we define two attachment sites, as one site doesn't do anything on its own besides bind integrases
#Create an integrase enumerator
bxb1_mechanism = IntegraseRule("Bxb1",
reactions={
("attB", "attP"): "attL",
("attP", "attB"): "attR"
})
bxb1 = Integrase_Enumerator(
"Bxb1", int_mechanisms={"Bxb1": bxb1_mechanism}
) #we must also define an integrase enumerator. The default integrase is always "int1", but here we are specifying "Bxb1" as the integrase. The Integrase enumerator gets a name, and the mechanism we defined above.
#create DNA_constructs with integrase sites
plasmid1_construct = DNA_construct([t16, attP, attB, gfp], circular=True)
genome_construct = DNA_construct([pconst, attB, rfp])
#Create a Mixture
myMixture = TxTlExtract(name="txtl",
parameters=parameters,
components=[plasmid1_construct, genome_construct],
global_component_enumerators=[bxb1])
#Test Recursion Depth = 0
#Note compile directives are used to speed up the test
myCRN0, comps0 = myMixture.compile_crn(recursion_depth=0,
return_enumerated_components=True,
initial_concentrations_at_end=True,
copy_objects=False,
add_reaction_species=False)
assert len(comps0) == 14
assert len(myCRN0.species) == 14
assert len(myCRN0.reactions) == 12
#Test recursion depth = 1
myCRN1, comps1 = myMixture.compile_crn(recursion_depth=1,
return_enumerated_components=True,
initial_concentrations_at_end=True,
copy_objects=False,
add_reaction_species=False)
assert len(comps1) == 85
assert len(myCRN1.species) == 52
assert len(myCRN1.reactions) == 97
#Recompiling at a different length doesn't change anything
myCRN0b, comps0b = myMixture.compile_crn(
recursion_depth=0,
return_enumerated_components=True,
initial_concentrations_at_end=True,
copy_objects=False,
add_reaction_species=False)
assert len(comps0) == len(comps0b)
assert myCRN0.species == myCRN0b.species
assert all([r in myCRN0.reactions for r in myCRN0b.reactions]) and all(
[r in myCRN0b.reactions for r in myCRN0.reactions])
def test_circular_DNAconstruct():
P = Promoter("pconst") #constitutive promoter
T = Terminator("term")
parameters = {
"cooperativity": 2,
"kb": 100,
"ku": 10,
"ktx": .05,
"ktl": .2,
"kdeg": 2,
"kint": .05
}
mechs = {
"transcription":
Transcription_MM(Species("RNAP", material_type="protein"))
}
#circular construct
x = DNA_construct([P, T],
mechanisms=mechs,
parameters=parameters,
circular=True)
y = x.enumerate_components()
assert (y[0] == x[0]) #correct promoter is returned
assert (
x[0].transcript == y[1].get_species()
) #promoter in the DNA_construct has the correct transcript species
assert (y[1].promoter == x[0]
) #rna is linked back to the DNA_construct's promoter
assert (y[1].promoter == y[0]
) #correct promoter is returned by enumerate_constructs
x = DNA_construct([[P, "reverse"], T],
mechanisms=mechs,
parameters=parameters,
circular=True)
y = x.enumerate_components()
assert (y[0] == x[0]) #correct promoter is returned
assert (
x[0].transcript == y[1].get_species()
) #promoter in the DNA_construct has the correct transcript species
assert (y[1].promoter == x[0]
) #rna is linked back to the DNA_construct's promoter
assert (y[1].promoter == y[0]
) #correct promoter is returned by enumerate_constructs
x = DNA_construct([
[P, "reverse"],
[T, "reverse"],
],
mechanisms=mechs,
parameters=parameters,
circular=True)
y = x.enumerate_components()
z = DNA_construct([T, P],
mechanisms=mechs,
parameters=parameters,
circular=True)
e = z.enumerate_components()
assert (y[1] == e[1]
) #different DNA constructs lead to the same RNA construct
assert (y[0] == x[0]) #correct promoter is working
assert (e[0] == z[1]) #correct promoter is working
def test_CRNPlotter():
class dummy_renderer:
class dummy_parts:
def __init__(self):
pass
def __init__(self, scale=1, linewidth=2):
self.linecolor = (0, 0, 0)
pass
def SBOL_part_renderers(self):
return self.dummy_parts()
def std_reg_renderers(self):
return self.dummy_parts()
def renderDNA(self, ax, designs, renderers, **keywords):
ax.plot([0], [1])
return (0, 100)
d_r = dummy_renderer()
test_plotter = CRNPlotter(dna_renderer=dummy_renderer(),
rna_renderer=dummy_renderer(),
cmap=[0, 1, 2, 3, 4, 5, 6])
test_construct = DNA_construct(
[Promoter("p1"),
IntegraseSite("attP", "attP"),
Terminator("t1")])
test_construct2 = DNA_construct(
[RBS("utr1"),
IntegraseSite("attB", "attB"),
Terminator("t1")])
test_construct3 = DNA_construct([
IntegraseSite("attL", "attL"),
IntegraseSite("attR", "attR"),
CDS("o1")
])
ts1 = test_construct.get_species()
test_species = Complex(
[ts1[1], Species("integrase", material_type="protein")]).parent
assert (test_plotter.part_dpl_dict == {})
assert (test_plotter.construct_dpl_dict == {})
assert (test_plotter.species_dpl_dict == {})
assert (test_plotter.species_image_dict == {})
test_plotter.make_dpls_from_construct(test_construct)
assert (len(test_plotter.part_dpl_dict) == len(test_construct)
) #new parts are added to the dictionary
assert (len(test_plotter.construct_dpl_dict) == 1
) #the new construct is added
#part added to part dict
assert (test_plotter.part_dpl_dict[Promoter("p1")].get_dpl()[0]['type'] ==
"Promoter")
#construct added to construct dict
condpl = test_plotter.construct_dpl_dict[test_construct].get_dpl()
#test that everything has the right type
assert (condpl[0]['type'] == "Promoter")
assert (condpl[1]['type'] == "RecombinaseSite")
assert (condpl[2]['type'] == "Terminator")
test_plotter.make_dpls_from_construct(test_construct2)
assert (len(test_plotter.part_dpl_dict) == len(test_construct) +
len(test_construct2) - 1)
#new parts from the new construct are added but the terminator is the same so don't add that one
assert (len(test_plotter.construct_dpl_dict) == 2
) #now there are two constructs
test_plotter.make_dpls_from_construct(test_construct3)
#almost all new parts are added
assert (len(test_plotter.part_dpl_dict) == len(test_construct) +
len(test_construct2) + len(test_construct3) - 1)
assert (len(test_plotter.construct_dpl_dict) == 3
) #there are now 3 constructs!
test_plotter.make_dpl_from_species(
test_species) #making dpl from single species
test_plotter.make_dpl_from_species(
Species("integrase", material_type="protein"))
assert (Species("integrase", material_type="protein")
in test_plotter.species_dpl_dict)
test_plotter.make_dpl_from_part(
RegulatedPromoter("p1", regulators=["r1", "r2"]))
assert (RegulatedPromoter("p1", regulators=["r1", "r2"])
in test_plotter.part_dpl_dict) #make a multipart promoter
#normal promoter is a multipart with a promoter being first
assert (test_plotter.part_dpl_dict[RegulatedPromoter(
"p1", regulators=["r1", "r2"])].get_dpl()[0]["type"] == "Promoter")
#try returning a reverse version of the same thing
boundspec = test_plotter.make_dpl_from_species(
Species("ooga", material_type="booga")
) #make a species to be bound to the promoter
revpart = test_plotter.part_dpl_dict[RegulatedPromoter(
"p1", regulators=["r1", "r2"])].get_directed(
"reverse",
bound=[boundspec]) #return reverse promoter with things bound
assert (revpart.get_dpl()[0]["type"] == "Operator"
) #reverse promoter has operators on the left
test_plotter.colordict = {"Promoter": "purple"}
prom_dpl = test_plotter.make_dpl_from_part(
Promoter("pconst")) #make a promoter part
assert (prom_dpl.color == "purple") #found the proper color
prom_dpl2 = test_plotter.make_dpl_from_part(
Promoter("funkbeast")) #make a different promoter part
assert (prom_dpl2.color == "purple")
rnadpl = test_plotter.make_dpl_from_species(
Species("testrna", material_type="rna"))
assert (rnadpl.dpl_type == "NCRNA")
#something is bound to the operator closest to the reversed promoter
assert (revpart.parts_list[1].bound is not None)
#construct having a multi-part promoter and a "user defined" part
test_construct4 = DNA_construct(
[RegulatedPromoter("p1", regulators=["r1", "r2"]),
DNA_part("test")])
test_plotter.make_dpl_from_species(test_construct4.get_species())
assert (test_construct4.get_species()
in test_plotter.species_dpl_dict) #construct is in the dictionary
rna_construct = RNA_construct([RBS("ooga"), CDS("booga")])
condpl1 = test_plotter.make_dpls_from_construct(rna_construct)
assert (condpl1.material_type == "rna") #material type is set correctly
rna_construct2 = RNA_construct([RBS("ooga"), CDS("booga")])
condpl2 = test_plotter.make_dpls_from_construct(rna_construct2)
assert (condpl2 == condpl1
) #this construct is already in the dictionary! Just return it
bound_construct = Complex([
test_construct4.get_species()[1],
Species("integrase", material_type="protein")
]).parent
#making a construct that is bound to something
dpl_binders = test_plotter.make_dpl_from_species(
bound_construct).get_dpl_binders()
#return the things that are bound
assert (dpl_binders[0][0]["type"] == "Binding")
test_plotter.make_dpl_from_species(
Complex([
Species("mydna", material_type="dna"),
Species("integrase", material_type="protein")
]))
#dpl made from a complex
#make sure the part inside the construct made it into the species dict
assert (Species("mydna", material_type="dna")
in test_plotter.species_dpl_dict)
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)
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)
from biocrnpyler import Promoter, ActivatablePromoter, RepressiblePromoter, RegulatedPromoter, CombinatorialPromoter
#list of possible promoter types
promoters = [
Promoter("promoter"),
ActivatablePromoter("activatable_promoter", activator=Species("A")),
RepressiblePromoter("repressible_promoter", repressor=Species("R")),
RegulatedPromoter("regulated_promoter",
regulators=[Species("S1"), Species("S2")]),
CombinatorialPromoter("combinatorial_promoter",
regulators=[Species("S1"),
Species("S2")])
]
from biocrnpyler import Terminator
#list of possible terminators
terminators = [Terminator("terminator")]
from biocrnpyler import SimpleTxTlExtract, TxTlExtract, SimpleTxTlDilutionMixture, TxTlDilutionMixture
#list of possible mixtures