diff --git a/syn_elong/model_changes.py b/syn_elong/model_changes.py index f189d41..d66edfa 100644 --- a/syn_elong/model_changes.py +++ b/syn_elong/model_changes.py @@ -14,7 +14,7 @@ import os import logging from cobra import Reaction, Metabolite -from concerto.utils.biolog_help import add_biolog_exchanges, universal_model +from concerto.utils.biolog_help import add_biolog_exchanges, load_universal_model from syn_elong.updates_from_ims837 import update_5 log = logging.getLogger() @@ -30,6 +30,8 @@ output_model_name = 'syn_elong.xml' output_model_path = os.path.join(_file_path, output_model_name) +universal_model = load_universal_model() + def write_model(model): cobra.io.write_sbml_model(model, output_model_path) @@ -79,7 +81,6 @@ def update_3(model): return model - def update_4(model): # adding reactions from gapfilling reaction_ids = {