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comparison COBRAxy/ras_to_bounds.py @ 116:734cc52537da draft

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author luca_milaz
date Sun, 13 Oct 2024 16:17:42 +0000
parents 867a965d6a57
children 69190617d1ea
comparison
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115:867a965d6a57 116:734cc52537da
122 mediumRxns_ids (list of str): List of reaction IDs in the medium. Their RAS is set to zero, but they are already set in the model. 122 mediumRxns_ids (list of str): List of reaction IDs in the medium. Their RAS is set to zero, but they are already set in the model.
123 Returns: 123 Returns:
124 None 124 None
125 """ 125 """
126 warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound)) 126 warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound))
127 warning(str(model.reactions.get_by_id("EX_Lcystin_e").upper_bound))
127 for reaction in rxns_ids: 128 for reaction in rxns_ids:
128 if reaction in ras_row.index: #and reaction not in mediumRxns_ids 129 if reaction in ras_row.index: #and reaction not in mediumRxns_ids
129 scaling_factor = ras_row[reaction] 130 scaling_factor = ras_row[reaction]
130 lower_bound=model.reactions.get_by_id(reaction).lower_bound 131 lower_bound=model.reactions.get_by_id(reaction).lower_bound
131 upper_bound=model.reactions.get_by_id(reaction).upper_bound 132 upper_bound=model.reactions.get_by_id(reaction).upper_bound
137 model.reactions.get_by_id(reaction).lower_bound=valMin 138 model.reactions.get_by_id(reaction).lower_bound=valMin
138 if upper_bound!=0 and lower_bound!=0: 139 if upper_bound!=0 and lower_bound!=0:
139 model.reactions.get_by_id(reaction).lower_bound=valMin 140 model.reactions.get_by_id(reaction).lower_bound=valMin
140 model.reactions.get_by_id(reaction).upper_bound=valMax 141 model.reactions.get_by_id(reaction).upper_bound=valMax
141 warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound)) 142 warning(str(model.reactions.get_by_id("EX_Lcystin_e").lower_bound))
143 warning(str(model.reactions.get_by_id("EX_Lcystin_e").upper_bound))
142 pass 144 pass
143 145
144 def process_ras_cell(cellName, ras_row, model, rxns_ids, mediumRxns_ids, output_folder): 146 def process_ras_cell(cellName, ras_row, model, rxns_ids, mediumRxns_ids, output_folder):
145 """ 147 """
146 Process a single RAS cell, apply bounds, and save the bounds to a CSV file. 148 Process a single RAS cell, apply bounds, and save the bounds to a CSV file.