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MultiQuercus.py
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import cobra
import os
from tests import TEST_DIR
from diel_models.diel_models_creator import diel_models_creator
def diel_multi_quercus(model):
diel_models_creator(model,
["C00089__cyto_Leaf", "C00089__cyto_Ibark", "C00089__cyto_Phellogen",
"C00059__cyto_Leaf", "C00059__cyto_Ibark", "C00059__cyto_Phellogen", "C00244__cyto_Leaf",
"C00244__cyto_Ibark", "C00244__cyto_Phellogen", "C00135__cyto_Leaf", "C00135__cyto_Ibark",
"C00135__cyto_Phellogen", "C00407__cyto_Leaf", "C00407__cyto_Ibark", "C00407__cyto_Phellogen",
"C00123__cyto_Leaf", "C00123__cyto_Ibark", "C00123__cyto_Phellogen", "C00073__cyto_Leaf",
"C00073__cyto_Ibark", "C00073__cyto_Phellogen", "C02265__cyto_Leaf", "C02265__cyto_Ibark",
"C02265__cyto_Phellogen", "C00188__cyto_Leaf", "C00188__cyto_Ibark", "C00188__cyto_Phellogen",
"C00525__cyto_Leaf", "C00525__cyto_Ibark", "C00525__cyto_Phellogen", "C00183__cyto_Leaf",
"C00183__cyto_Ibark", "C00183__cyto_Phellogen", "C00062__cyto_Leaf", "C00062__cyto_Ibark",
"C00062__cyto_Phellogen", "C00491__cyto_Leaf", "C00491__cyto_Ibark", "C00491__cyto_Phellogen",
"C00064__cyto_Leaf", "C00064__cyto_Ibark", "C00064__cyto_Phellogen", "C00037__cyto_Leaf",
"C00037__cyto_Ibark", "C00037__cyto_Phellogen", "C00148__cyto_Leaf", "C00148__cyto_Ibark",
"C00148__cyto_Phellogen", "C00082__cyto_Leaf", "C00082__cyto_Ibark", "C00082__cyto_Phellogen",
"C01401__cyto_Ibark", "C01401__cyto_Phellogen", "C00025__cyto_Leaf",
"C00025__cyto_Ibark", "C00025__cyto_Phellogen", "C00152__cyto_Leaf", "C00152__cyto_Ibark",
"C00152__cyto_Phellogen", "C00065__cyto_Leaf", "C00065__cyto_Ibark", "C00065__cyto_Phellogen",
"C00369__cyto_Leaf", "C00369__cyto_Ibark", "C00369__cyto_Phellogen", "C02336__cyto_Leaf",
"C02336__cyto_Ibark", "C02336__cyto_Phellogen", "C00208__cyto_Leaf", "C00208__cyto_Ibark",
"C00208__cyto_Phellogen", "C00122__cyto_Leaf", "C00122__cyto_Ibark", "C00122__cyto_Phellogen",
"C00158__cyto_Leaf", "C00158__cyto_Ibark", "C00158__cyto_Phellogen"],
["EX_C00205__dra"], ["EX_C00244__dra"], "Total_biomass",
['Leaf', 'Ibark', 'Phellogen'])
cobra.io.write_sbml_model(model, os.path.join(TEST_DIR, 'models', 'diel_multi_quercus_model.xml'))
if __name__ == '__main__':
multi_quercus_model_path = os.path.join(TEST_DIR, 'models', 'MultiTissueQuercusModel.xml')
multi_quercus_model = cobra.io.read_sbml_model(multi_quercus_model_path)
diel_multi_quercus(multi_quercus_model)