def to_gnomic(self):
if _gnomic_available_:
return Genotype([target.to_gnomic() for target in self.targets])
else:
raise SystemError(
"Gnomic is only compatible with python >= 3 (%i.%i)" %
(sys.version_info.major, sys.version_info.minor))
def test_gnomic_integration_FluxModulationTarget(self, model):
# with pytest.raises(ValueError):
# FluxModulationTarget("test", 0, 0) # TODO: this should really not be possible
flux_modulation_target = FluxModulationTarget("test", 1, 0)
flux_modulation_target_gnomic = flux_modulation_target.to_gnomic()
assert genotype_to_string(Genotype([flux_modulation_target_gnomic
])) == "+flux.test(value=1)"
flux_modulation_target = FluxModulationTarget("PGK",
0.5,
1,
accession_id="PGK",
accession_db="bigg")
flux_modulation_target_gnomic = flux_modulation_target.to_gnomic()
assert genotype_to_string(Genotype([
flux_modulation_target_gnomic
])) == "+flux.PGK(value=0.5)#bigg:PGK"
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_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()
assert genotype_to_string(Genotype([
swap_target_gnomic
])) == "+reaction.GAPD(nad_c=nadp_c;nadh_c=nadph_c)"
def test_gene_knockout_target(self, model):
gene = "b4025"
knockout_target = GeneKnockoutTarget(gene,
accession_id=gene,
accession_db='bigg')
knockout_target_gnomic = knockout_target.to_gnomic()
assert genotype_to_string(Genotype([knockout_target_gnomic
])) == "-b4025#bigg:b4025"
with model:
knockout_target.apply(model)
assert model.reactions.PGI.lower_bound == 0
assert model.reactions.PGI.upper_bound == 0
assert abs(model.optimize().f - 0.8631) < 0.0001
assert model.reactions.PGI.lower_bound == -1000
assert model.reactions.PGI.upper_bound == 1000
def to_gnomic(self):
return Genotype([target.to_gnomic() for target in self.targets])
def _repr_html_(self):
return genotype_to_text(Genotype([self.to_gnomic()]))
def __str__(self):
return genotype_to_string(Genotype([self.to_gnomic()]))
