Misc

Reorder model reactions

By providing a list with the new reaction order, you can re-order the reactions in all model sheets.

from set_up_grasp_models.set_up_models.manipulate_model import reorder_reactions

# list with reaction order
rxn_order = ['R_PGL', 'R_EDD', 'R_EDA', 'R_PGI', 'R_FBP', 'R_FBA', 'R_TPI', 'R_GAPD',
             'R_PGK', 'R_PGM', 'R_ENO', 'R_PYK', 'R_G6PDH2','R_EX_pyr', 'R_EX_pep',
             'R_EX_g6p', 'R_EX_6pgc', 'R_EX_g3p', 'R_EX_f6p', 'R_EX_3pg']

# path to current model
model_name = 'glycolysis_v2'
file_in = os.path.join('example_files', 'output', model_name + '.xlsx')

# import current model with pandas
data_dict = pd.read_excel(file_in, sheet_name=None, index_col=0)

# path to the model with re-ordered reactions - just substitute current one
file_out = file_in

# re-order reactions according to rxn_list
reorder_reactions(data_dict, rxn_order, file_out)

Remove leading and trailing spaces

This function removes all leading and trailing spaces from string fields.

from set_up_grasp_models.set_up_models.manipulate_model import remove_spaces

# path to current model
model_name = 'glycolysis_v2'
file_in = os.path.join('example_files', 'output', model_name + '.xlsx')

# import current model with pandas
data_dict = pd.read_excel(file_in, sheet_name=None, index_col=0)

# path to the model with re-ordered reactions - just substitute current one
file_out = file_in

# remove any leading or trailing spaces in all string cells
remove_spaces(data_dict, file_out)

Rename columns in the model

Since this package assumes certain column names, it is important that they are correct. To make sure just run:

from set_up_grasp_models.set_up_models.manipulate_model import rename_columns

# path to current model
model_name = 'glycolysis_v2'
file_in = os.path.join('example_files', 'output', model_name + '.xlsx')

# import current model with pandas
data_dict = pd.read_excel(file_in, sheet_name=None, index_col=0)

# path to the model with re-ordered reactions - just substitute current one
file_out = file_in

# remove any leading or trailing spaces in all string cells
rename_columns(data_dict, file_out)

This will rename all columns to standard names.

Convert model .m file to ODE format

The matlab file in which the model is specified cannot be used as input to matlab’s ODE solvers.

This function takes in that matlab file and converts it into a format that can be given as input to matlab’s ODE solvers.

from set_up_grasp_models.set_up_models.set_up_ode_model import convert_to_ode_model

model_name = 'glycolysis_v2'
file_in = os.path.join('example_files', 'output', model_name + '_Kinetics1.m')

convert_to_ode_model(file_in)