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_gnomic_integration_ReactionCofactorSwapTarget(self, model):
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()
expected = "reaction.GAPD(cofactors=nadp_c,nadph_c)"
assert genotype_to_string(Genotype([swap_target_gnomic])) == expected
def test_reaction_cofactor_swap_target(self, model):
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)
with model:
swap_target.apply(model)
assert model.metabolites.nad_c not in model.reactions.GAPD.metabolites
assert model.metabolites.nadh_c not in model.reactions.GAPD.metabolites
assert model.metabolites.nadp_c in model.reactions.GAPD.metabolites
assert model.metabolites.nadph_c in model.reactions.GAPD.metabolites
assert model.metabolites.nadp_c not in model.reactions.GAPD.metabolites
assert model.metabolites.nadph_c not in model.reactions.GAPD.metabolites
assert model.metabolites.nad_c in model.reactions.GAPD.metabolites
assert model.metabolites.nadh_c in model.reactions.GAPD.metabolites
swap_target = ReactionCofactorSwapTarget("GND", swap_pairs)
with model:
swap_target.apply(model)
assert model.metabolites.nad_c in model.reactions.GND.metabolites
assert model.metabolites.nadh_c in model.reactions.GND.metabolites
assert model.metabolites.nadp_c not in model.reactions.GND.metabolites
assert model.metabolites.nadph_c not in model.reactions.GND.metabolites
assert model.metabolites.nadp_c in model.reactions.GND.metabolites
assert model.metabolites.nadph_c in model.reactions.GND.metabolites
assert model.metabolites.nad_c not in model.reactions.GND.metabolites
assert model.metabolites.nadh_c not in model.reactions.GND.metabolites
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 _generate_designs(swaps, swap_pair):
designs = []
for swap_design, _ in swaps:
designs.append(
StrainDesign([
ReactionCofactorSwapTarget(swap, swap_pair)
for swap in swap_design
]))
return designs
def test_invalid_reaction_cofactor_swap_target(self, model):
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_124", swap_pairs)
with pytest.raises(KeyError):
swap_target.apply(model)
swap_target = ReactionCofactorSwapTarget("ACKr", swap_pairs)
with pytest.raises(ValueError):
swap_target.apply(model)
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'