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'