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.