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(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'