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quercus_reactions_fluxes.py
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import os
import cobra
from tests import TEST_DIR
from cobra.flux_analysis import pfba
import pandas as pd
def validate_reactions_fluxes(original_model, diel_model, original_multitissue_model, diel_multitissue_model):
original_model.objective = "EX_C00205__dra"
original_model.objective_direction = "max"
original_single_carboxylation = original_model.reactions.get_by_id("R00024__chlo")
original_single_oxygenation = original_model.reactions.get_by_id("R03140__chlo")
same_flux = original_model.problem.Constraint(
original_single_carboxylation.flux_expression * 1 -
original_single_oxygenation.flux_expression * 3, lb=0, ub=0)
original_model.add_cons_vars(same_flux)
original_solution = pfba(original_model).fluxes
original_multitissue_model.objective = "EX_C00205__dra"
original_multitissue_model.objective_direction = "max"
original_multi_carboxylation = original_multitissue_model.reactions.get_by_id("R00024__plst_Leaf")
original_multi_oxygenation = original_multitissue_model.reactions.get_by_id("R03140__plst_Leaf")
same_flux = original_multitissue_model.problem.Constraint(
original_multi_carboxylation.flux_expression * 1 -
original_multi_oxygenation.flux_expression * 3, lb=0, ub=0)
original_multitissue_model.add_cons_vars(same_flux)
original_multitissue_solution = pfba(original_multitissue_model).fluxes
diel_model.objective = "EX_C00205__dra_Day"
diel_model.objective_direction = "max"
diel_model.reactions.get_by_id("Biomass_Total").bounds = (0.11, 0.11)
diel_carboxylation_day = diel_model.reactions.get_by_id("R00024__chlo_Day")
diel_oxygenation_day = diel_model.reactions.get_by_id("R03140__chlo_Day")
same_flux = diel_model.problem.Constraint(
diel_carboxylation_day.flux_expression * 1 -
diel_oxygenation_day.flux_expression * 3, lb=0, ub=0)
diel_model.add_cons_vars(same_flux)
diel_carboxylation_night = diel_model.reactions.get_by_id("R00024__chlo_Night")
diel_oxygenation_night = diel_model.reactions.get_by_id("R03140__chlo_Night")
same_flux = diel_model.problem.Constraint(
diel_carboxylation_night.flux_expression * 1 -
diel_oxygenation_night.flux_expression * 3, lb=0, ub=0)
diel_model.add_cons_vars(same_flux)
diel_solution = pfba(diel_model).fluxes
diel_multitissue_model.reactions.get_by_id("Biomass_Total").bounds = (0.11, 0.11)
diel_multitissue_model.reactions.EX_C00205__dra_Day.bounds = (-1000, 1000)
diel_multitissue_model.objective = "EX_C00205__dra_Day"
diel_multitissue_model.objective_direction = "max"
diel_multi_carboxylation_day = diel_multitissue_model.reactions.get_by_id("R00024__plst_Leaf_Day")
diel_multi_oxygenation_day = diel_multitissue_model.reactions.get_by_id("R03140__plst_Leaf_Day")
same_flux_day = diel_multitissue_model.problem.Constraint(
diel_multi_carboxylation_day.flux_expression * 1 -
diel_multi_oxygenation_day.flux_expression * 3, lb=0, ub=0)
diel_multitissue_model.add_cons_vars(same_flux_day)
diel_multi_carboxylation_night = diel_multitissue_model.reactions.get_by_id("R00024__plst_Leaf_Night")
diel_multi_oxygenation_night = diel_multitissue_model.reactions.get_by_id("R03140__plst_Leaf_Night")
same_flux_night = diel_multitissue_model.problem.Constraint(
diel_multi_carboxylation_night.flux_expression * 1 -
diel_multi_oxygenation_night.flux_expression * 3, lb=0, ub=0)
diel_multitissue_model.add_cons_vars(same_flux_night)
diel_multitissue_solution = pfba(diel_multitissue_model).fluxes
data = {'RuBisCO + O2': [original_solution["R03140__chlo"],
original_multitissue_solution["R03140__plst_Leaf"],
diel_solution["R03140__chlo_Day"], diel_solution["R03140__chlo_Night"],
diel_multitissue_solution["R03140__plst_Leaf_Day"],
diel_multitissue_solution["R03140__plst_Leaf_Night"]],
'RuBisCO + CO2': [original_solution["R00024__chlo"],
original_multitissue_solution["R00024__plst_Leaf"],
diel_solution["R00024__chlo_Day"], diel_solution["R00024__chlo_Night"],
diel_multitissue_solution["R00024__plst_Leaf_Day"],
diel_multitissue_solution["R00024__plst_Leaf_Night"]],
'Photosystem_I': [original_solution["Photosystem_I__chlo"],
original_multitissue_solution["Photosystem_I__plst_Leaf"],
diel_solution["Photosystem_I__chlo_Day"], diel_solution["Photosystem_I__chlo_Night"],
diel_multitissue_solution["Photosystem_I__plst_Leaf_Day"],
diel_multitissue_solution["Photosystem_I__plst_Leaf_Night"]],
'Glicerate-3P to 1,3Bisphosphoglicerate': [original_solution["R01512__cyto"],
original_multitissue_solution["R01512__plst_Leaf"],
diel_solution["R01512__cyto_Day"],
diel_solution["R01512__cyto_Night"],
diel_multitissue_solution["R01512__plst_Leaf_Day"],
diel_multitissue_solution["R01512__plst_Leaf_Night"]],
'1,3Bisphosphoglicerate to G3P': [original_solution["R01063__chlo"],
original_multitissue_solution["R01063__plst_Leaf"],
diel_solution["R01063__chlo_Day"],
diel_solution["R01063__chlo_Night"],
diel_multitissue_solution["R01063__plst_Leaf_Day"],
diel_multitissue_solution["R01063__plst_Leaf_Night"]],
'G3P to Glycerone-P': [original_solution["R01015__cyto"],
original_multitissue_solution["R01015__plst_Leaf"],
diel_solution["R01015__cyto_Day"], diel_solution["R01015__cyto_Night"],
diel_multitissue_solution["R01015__plst_Leaf_Day"],
diel_multitissue_solution["R01015__plst_Leaf_Night"]],
'Glycerone-P to Sedoheptulose1,7-bisphosphate': [original_solution["R01829__cyto"],
original_multitissue_solution["R01829__plst_Leaf"],
diel_solution["R01829__cyto_Day"],
diel_solution["R01829__cyto_Night"],
diel_multitissue_solution["R01829__plst_Leaf_Day"],
diel_multitissue_solution["R01829__plst_Leaf_Night"]],
'Sedoheptulose1,7-bisphosphate to Sedoheptulose7-phosphate': [original_solution["R01845__cyto"],
original_multitissue_solution[
"R01845__plst_Leaf"],
diel_solution["R01845__cyto_Day"],
diel_solution["R01845__cyto_Night"],
diel_multitissue_solution[
"R01845__plst_Leaf_Day"],
diel_multitissue_solution[
"R01845__plst_Leaf_Night"]],
'Sedoheptulose7-phosphate to R5P': [original_solution["R01641__cyto"],
original_multitissue_solution["R01641__plst_Leaf"],
diel_solution["R01641__cyto_Day"], diel_solution["R01641__cyto_Night"],
diel_multitissue_solution["R01641__plst_Leaf_Day"],
diel_multitissue_solution["R01641__plst_Leaf_Night"]],
'R5P to Ri5P': [original_solution["R01056__cyto"],
original_multitissue_solution["R01056__plst_Leaf"],
diel_solution["R01056__cyto_Day"], diel_solution["R01056__cyto_Night"],
diel_multitissue_solution["R01056__plst_Leaf_Day"],
diel_multitissue_solution["R01056__plst_Leaf_Night"]],
'Ri5P to Ri15P2': [original_solution["R01523__chlo"],
original_multitissue_solution["R01523__plst_Leaf"],
diel_solution["R01523__chlo_Day"], diel_solution["R01523__chlo_Night"],
diel_multitissue_solution["R01523__plst_Leaf_Day"],
diel_multitissue_solution["R01523__plst_Leaf_Night"]]
}
tabel = pd.DataFrame(data)
tabel.index = ["Quercus", "Quercus Multi Tissue", "Day Quercus", "Night Quercus", "Day Multi Quercus",
"Night Multi Quercus"]
tabel.to_csv('Quercus_Reactions_Fluxes.csv', sep=',')
print(tabel)
if __name__ == '__main__':
original_model = cobra.io.read_sbml_model(os.path.join(TEST_DIR, 'models', 'QuercusSuberGeneralModel.xml'))
diel_model = cobra.io.read_sbml_model(os.path.join(TEST_DIR, 'models', "diel_quercus_model.xml"))
original_multitissue_model = cobra.io.read_sbml_model(
os.path.join(TEST_DIR, 'models', "MultiTissueQuercusModel.xml"))
diel_multitissue_model = cobra.io.read_sbml_model(os.path.join(TEST_DIR, 'models', "diel_multi_quercus_model.xml"))
validate_reactions_fluxes(original_model, diel_model, original_multitissue_model, diel_multitissue_model)