def test_incompatible_targets(self):
ko_target = ReactionKnockoutTarget("a")
ki_target = ReactionKnockinTarget("a", None)
with pytest.raises(IncompatibleTargets):
EnsembleTarget("a", [ko_target, ki_target])
with pytest.raises(IncompatibleTargets):
EnsembleTarget("a", [ki_target, ko_target])
ko_target = ReactionKnockoutTarget("b")
swap_target = ReactionCofactorSwapTarget("b", [("nad_c", "nadh_c"),
("nadp_c", "nadph_c")])
with pytest.raises(IncompatibleTargets):
EnsembleTarget("b", [ko_target, swap_target])
with pytest.raises(IncompatibleTargets):
EnsembleTarget("b", [swap_target, ko_target])
modulation_target = ReactionModulationTarget("c", 0, 0)
ki_target = ReactionKnockinTarget("c", None)
with pytest.raises(IncompatibleTargets):
EnsembleTarget("c", [modulation_target, ki_target])
with pytest.raises(IncompatibleTargets):
EnsembleTarget("c", [ki_target, modulation_target])
def test_compatible_targets(self):
modulation_target = ReactionModulationTarget("a", 1, 0)
ki_target = ReactionKnockinTarget("a", None)
ensemble_1 = EnsembleTarget("a", [modulation_target, ki_target])
ensemble_2 = EnsembleTarget("a", [ki_target, modulation_target])
assert ensemble_1.targets == ensemble_2.targets
modulation_target = ReactionModulationTarget("b", 1, 0)
swap_target = ReactionCofactorSwapTarget("b", [("nad_c", "nadh_c"),
("nadp_c", "nadph_c")])
ensemble_1 = EnsembleTarget("b", [modulation_target, swap_target])
ensemble_2 = EnsembleTarget("b", [swap_target, modulation_target])
assert ensemble_1.targets == ensemble_2.targets
ki_target = ReactionKnockinTarget("c", None)
modulation_target = ReactionModulationTarget("c", 1, 0)
swap_target = ReactionCofactorSwapTarget("c", [("nad_c", "nadh_c"),
("nadp_c", "nadph_c")])
ensemble = EnsembleTarget("c",
[modulation_target, swap_target, ki_target])
assert ensemble.targets[0] == ki_target
assert ensemble.targets[1] == swap_target
assert ensemble.targets[2] == modulation_target
def test_reaction_knock_in_target(self, model):
reaction = Reaction(id="atpzase", name="Cosmic ATP generator")
atp_z = Metabolite(id="atp_z", name="Cosmic ATP", compartment="c")
reaction.add_metabolites({model.metabolites.atp_c: 1, atp_z: -1})
knockin_target = ReactionKnockinTarget("atpzase", reaction)
with model:
knockin_target.apply(model)
assert atp_z in model.metabolites
assert reaction in model.reactions
assert atp_z not in model.metabolites
assert reaction not in model.reactions
def _build_targets(self):
targets = DictList()
for reaction in self.reactions:
reaction = self._replace_adapted_metabolites(reaction)
targets.append(ReactionKnockinTarget(reaction.id, reaction))
for reaction in self.exchanges:
reaction = self._replace_adapted_metabolites(reaction)
targets.append(ReactionKnockinTarget(reaction.id, reaction))
product = self._replace_adapted_metabolites(self.product)
product.lower_bound = 0
targets.append(ReactionKnockinTarget(product.id, product))
return targets
def test_add_strain_design(self):
t1 = ReactionKnockoutTarget('PGI')
t2 = ReactionKnockoutTarget('GAPD')
t3 = ReactionKnockinTarget("CAD", self.cad_reaction)
strain_design1 = StrainDesign([t1, t2, t3])
t4 = ReactionModulationTarget("PGI", 5, 1)
strain_design2 = StrainDesign([t4])
self.assertRaises(IncompatibleTargets, strain_design1.__add__, strain_design2)
self.assertRaises(IncompatibleTargets, strain_design2.__add__, strain_design1)
self.assertRaises(IncompatibleTargets, strain_design1.__iadd__, strain_design2)
self.assertRaises(IncompatibleTargets, strain_design2.__iadd__, strain_design1)
t5 = ReactionModulationTarget("RPI", 2, 0)
strain_design3 = StrainDesign([t5])
strain_design4 = strain_design3 + strain_design1
self.assertIn(t1, strain_design4)
self.assertIn(t2, strain_design4)
self.assertIn(t3, strain_design4)
self.assertNotIn(t4, strain_design4)
self.assertIn(t5, strain_design4)
strain_design3 += strain_design1
self.assertIn(t1, strain_design3)
self.assertIn(t2, strain_design3)
self.assertIn(t3, strain_design3)
self.assertNotIn(t4, strain_design3)
self.assertIn(t5, strain_design3)
def __init__(self, reactions, exchanges, adapters, product, *args,
**kwargs):
self._meta_information = MetaInformation()
self.reactions = reactions
self.targets = [
ReactionKnockinTarget(reaction.id, reaction)
for reaction in reactions
]
self.exchanges = exchanges
self.adapters = adapters
self.product = product
def _build_targets(self):
targets = DictList()
for reaction in self.reactions:
reaction = self._replace_adapted_metabolites(reaction)
if reaction.id in metanetx.mnx2all:
target = ReactionKnockinTarget(reaction.id,
reaction,
accession_id=reaction.id,
accession_db='metanetx')
else:
target = ReactionKnockinTarget(reaction.id, reaction)
targets.append(target)
for reaction in self.exchanges:
reaction = self._replace_adapted_metabolites(reaction)
targets.append(ReactionKnockinTarget(reaction.id, reaction))
product = self._replace_adapted_metabolites(self.product)
product.lower_bound = 0
targets.append(ReactionKnockinTarget(product.id, product))
return targets
def test_design_to_gnomic(self, cad_reaction):
from gnomic import Genotype
t1 = ReactionKnockoutTarget('PGI')
t2 = ReactionKnockoutTarget('GAPD')
t3 = ReactionKnockinTarget("CAD", cad_reaction)
strain_design1 = StrainDesign([t1, t2, t3])
sd_gnomic = strain_design1.to_gnomic()
assert isinstance(sd_gnomic, Genotype)
assert len(sd_gnomic.added_features) == 1
assert len(sd_gnomic.removed_features) == 2
def test_design_to_gnomic(self):
from gnomic import Genotype
t1 = ReactionKnockoutTarget('PGI')
t2 = ReactionKnockoutTarget('GAPD')
t3 = ReactionKnockinTarget("CAD", self.cad_reaction)
strain_design1 = StrainDesign([t1, t2, t3])
sd_gnomic = strain_design1.to_gnomic()
self.assertIsInstance(sd_gnomic, Genotype)
self.assertEqual(len(sd_gnomic.added_features), 1)
self.assertEqual(len(sd_gnomic.removed_features), 2)
def test_create_strain_design(self, cad_reaction):
t1 = ReactionKnockoutTarget('PGI')
t2 = ReactionKnockoutTarget('GAPD')
t3 = ReactionKnockinTarget("CAD", cad_reaction)
strain_design = StrainDesign([t1, t2, t3])
assert len(strain_design) == 3
strain_design2 = StrainDesign([t1, t2, t3])
strain_design3 = StrainDesign([t2, t1, t3])
assert strain_design == strain_design2
assert strain_design == strain_design3
assert strain_design3 == strain_design2
assert t1 in strain_design
assert t2 in strain_design
assert t3 in strain_design
def test_create_strain_design(self):
t1 = ReactionKnockoutTarget('PGI')
t2 = ReactionKnockoutTarget('GAPD')
t3 = ReactionKnockinTarget("CAD", self.cad_reaction)
strain_design = StrainDesign([t1, t2, t3])
self.assertEqual(len(strain_design), 3)
strain_design2 = StrainDesign([t1, t2, t3])
strain_design3 = StrainDesign([t2, t1, t3])
self.assertEqual(strain_design, strain_design2)
self.assertEqual(strain_design, strain_design3)
self.assertEqual(strain_design3, strain_design2)
self.assertIn(t1, strain_design)
self.assertIn(t2, strain_design)
self.assertIn(t3, strain_design)
def test_gnomic_integration_ReactionKnockinTarget(self, model):
reaction = Reaction(id="atpzase", name="Cosmic ATP generator")
atp_z = Metabolite(id="atp_z", name="Cosmic ATP", compartment="c")
reaction.add_metabolites({model.metabolites.atp_c: 1, atp_z: -1})
knockin_target = ReactionKnockinTarget("atpzase", reaction)
knockin_target_gnomic = knockin_target.to_gnomic()
assert genotype_to_string(Genotype([knockin_target_gnomic])) == "+reaction.atpzase"
reaction.add_metabolites({model.metabolites.atp_c: 1, atp_z: -1})
knockin_target = ReactionKnockinTarget("atpzase", reaction, accession_id='atpzase', accession_db='unicorn')
knockin_target_gnomic = knockin_target.to_gnomic()
assert genotype_to_string(Genotype([knockin_target_gnomic])) == "+reaction.atpzase#unicorn:atpzase"
def test_add_strain_design(self, cad_reaction):
t1 = ReactionKnockoutTarget('PGI')
t2 = ReactionKnockoutTarget('GAPD')
t3 = ReactionKnockinTarget("CAD", cad_reaction)
strain_design1 = StrainDesign([t1, t2, t3])
t4 = ReactionModulationTarget("PGI", 5, 1)
strain_design2 = StrainDesign([t4])
with pytest.raises(IncompatibleTargets):
strain_design1.__add__(strain_design2)
with pytest.raises(IncompatibleTargets):
strain_design2.__add__(strain_design1)
with pytest.raises(IncompatibleTargets):
strain_design1.__iadd__(strain_design2)
with pytest.raises(IncompatibleTargets):
strain_design2.__iadd__(strain_design1)
t5 = ReactionModulationTarget("RPI", 2, 0)
strain_design3 = StrainDesign([t5])
strain_design4 = strain_design3 + strain_design1
assert t1 in strain_design4
assert t2 in strain_design4
assert t3 in strain_design4
assert t4 not in strain_design4
assert t5 in strain_design4
strain_design3 += strain_design1
assert t1 in strain_design3
assert t2 in strain_design3
assert t3 in strain_design3
assert t4 not in strain_design3
assert t5 in strain_design3
def test_gnomic_integration(self, model):
from gnomic.models import Accession, Feature, Mutation, FeatureTree
abstract_target = Target("test")
abstract_target_gnomic = abstract_target.to_gnomic()
assert isinstance(abstract_target_gnomic, Accession)
assert abstract_target_gnomic.identifier == abstract_target.id
flux_modulation_target = FluxModulationTarget("test", 1, 0)
flux_modulation_target_gnomic = flux_modulation_target.to_gnomic()
flux_mod_new = flux_modulation_target_gnomic.new
flux_mod_old = flux_modulation_target_gnomic.old
assert isinstance(flux_modulation_target_gnomic, Mutation)
assert isinstance(flux_mod_old, FeatureTree)
assert isinstance(flux_mod_old[0], Feature)
assert flux_mod_old[
0].accession.identifier == flux_modulation_target.id
assert flux_mod_old[0].variant is None
assert flux_mod_old[0].type == 'flux'
assert isinstance(flux_mod_new, FeatureTree)
assert isinstance(flux_mod_new[0], Feature)
assert flux_mod_new[
0].accession.identifier == flux_modulation_target.id
assert flux_mod_new[0].type == 'flux'
assert flux_mod_new[
0].variant == "over-expression(%.3f)" % flux_modulation_target.fold_change
flux_modulation_target = FluxModulationTarget("test", 0.5, 1)
flux_modulation_target_gnomic = flux_modulation_target.to_gnomic()
flux_mod_new = flux_modulation_target_gnomic.new
flux_mod_old = flux_modulation_target_gnomic.old
assert isinstance(flux_modulation_target_gnomic, Mutation)
assert isinstance(flux_mod_old, FeatureTree)
assert isinstance(flux_mod_old[0], Feature)
assert flux_mod_old[
0].accession.identifier == flux_modulation_target.id
assert flux_mod_old[0].variant is None
assert flux_mod_old[0].type == 'flux'
assert isinstance(flux_mod_new, FeatureTree)
assert isinstance(flux_mod_new[0], Feature)
assert flux_mod_new[
0].accession.identifier == flux_modulation_target.id
assert flux_mod_new[0].type == 'flux'
assert flux_mod_new[
0].variant == "down-regulation(%.3f)" % flux_modulation_target.fold_change
flux_modulation_target = FluxModulationTarget("test", 0, 1)
flux_modulation_target_gnomic = flux_modulation_target.to_gnomic()
assert isinstance(flux_modulation_target_gnomic, Mutation)
assert isinstance(flux_modulation_target_gnomic.old, FeatureTree)
assert isinstance(flux_modulation_target_gnomic.old[0], Feature)
assert flux_modulation_target_gnomic.old[
0].accession.identifier == flux_modulation_target.id
assert flux_modulation_target_gnomic.old[0].variant is None
assert flux_modulation_target_gnomic.old[0].type == 'flux'
assert flux_modulation_target_gnomic.new is None
reaction = Reaction(id="atpzase", name="Cosmic ATP generator")
atp_z = Metabolite(id="atp_z", name="Cosmic ATP", compartment="c")
reaction.add_metabolites({model.metabolites.atp_c: 1, atp_z: -1})
knockin_target = ReactionKnockinTarget("atpzase", reaction)
knockin_target_gnomic = knockin_target.to_gnomic()
assert isinstance(knockin_target_gnomic, Mutation)
assert isinstance(knockin_target_gnomic.new, FeatureTree)
assert isinstance(knockin_target_gnomic.new[0], Feature)
assert knockin_target_gnomic.new[
0].accession.identifier == knockin_target.id
assert knockin_target_gnomic.new[0].variant is None
assert knockin_target_gnomic.new[0].type == 'reaction'
assert knockin_target_gnomic.old is None
cofactor_id_swaps = [("nad_c", "nadh_c"), ("nadp_c", "nadph_c")]
swap_pairs = ([
model.metabolites.get_by_id(m) for m in cofactor_id_swaps[0]
], [model.metabolites.get_by_id(m) for m in cofactor_id_swaps[1]])
swap_target = ReactionCofactorSwapTarget("GAPD", swap_pairs)
swap_target_gnomic = swap_target.to_gnomic()
assert isinstance(swap_target_gnomic, Mutation)
assert isinstance(swap_target_gnomic.old, FeatureTree)
assert isinstance(swap_target_gnomic.old[0], Feature)
assert swap_target_gnomic.old[0].accession.identifier == swap_target.id
assert swap_target_gnomic.old[0].variant is None
assert swap_target_gnomic.old[0].type == 'reaction'
assert isinstance(swap_target_gnomic.new, FeatureTree)
assert isinstance(swap_target_gnomic.new[0], Feature)
assert swap_target_gnomic.new[
0].accession.identifier == swap_target.id + swap_target.swap_str
assert swap_target_gnomic.new[0].variant is None
assert swap_target_gnomic.new[0].type == 'reaction'