Mercurial > repos > bimib > cobraxy

comparison COBRAxy/utils/general_utils.py @ 412:bdf4630ac1eb draft

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author francesco_lapi
date Mon, 08 Sep 2025 21:24:32 +0000
parents 6b015d3184ab
children 7a3ccf066b2c
comparison
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411:6b015d3184ab 412:bdf4630ac1eb
15 15
16 import zipfile 16 import zipfile
17 import gzip 17 import gzip
18 import bz2 18 import bz2
19 from io import StringIO 19 from io import StringIO
20 import rule_parsing as rulesUtils 20 import utils.rule_parsing as rulesUtils
21 import reaction_parsing as reactionUtils 21 import utils.reaction_parsing as reactionUtils
22 22
23 23
24 24
25 class ValueErr(Exception): 25 class ValueErr(Exception):
26 def __init__(self, param_name, expected, actual): 26 def __init__(self, param_name, expected, actual):
775 775
776 print(f"Aggiunti {len(metabolites_dict)} metaboliti e {len(compartments_dict)} compartimenti") 776 print(f"Aggiunti {len(metabolites_dict)} metaboliti e {len(compartments_dict)} compartimenti")
777 777
778 # Seconda passata: aggiungi le reazioni 778 # Seconda passata: aggiungi le reazioni
779 reactions_added = 0 779 reactions_added = 0
780 reactions_skipped = 0
781 780
782 for idx, row in df.iterrows(): 781 for idx, row in df.iterrows():
782 reaction_id = str(row['ReactionID']).strip()
783 reaction_formula = str(row['Reaction']).strip()
784
785 # Salta reazioni senza formula
786 if not reaction_formula or reaction_formula == 'nan':
787 raise ValueError(f"Formula della reazione mancante {reaction_id}")
788
789 # Crea la reazione
790 reaction = Reaction(reaction_id)
791 reaction.name = reaction_id
792
793 # Imposta bounds
794 reaction.lower_bound = float(row['lower_bound']) if pd.notna(row['lower_bound']) else -1000.0
795 reaction.upper_bound = float(row['upper_bound']) if pd.notna(row['upper_bound']) else 1000.0
796
797 # Aggiungi gene rule se presente
798 if pd.notna(row['Rule']) and str(row['Rule']).strip():
799 reaction.gene_reaction_rule = str(row['Rule']).strip()
800
801 # Parse della formula della reazione
783 try: 802 try:
784 reaction_id = str(row['ReactionID']).strip() 803 parse_reaction_formula(reaction, reaction_formula, metabolites_dict)
785 reaction_formula = str(row['Reaction']).strip()
786
787 # Salta reazioni senza formula
788 if not reaction_formula or reaction_formula == 'nan':
789 reactions_skipped += 1
790 continue
791
792 # Crea la reazione
793 reaction = Reaction(reaction_id)
794 reaction.name = reaction_id
795
796 # Imposta bounds
797 reaction.lower_bound = float(row['lower_bound']) if pd.notna(row['lower_bound']) else -1000.0
798 reaction.upper_bound = float(row['upper_bound']) if pd.notna(row['upper_bound']) else 1000.0
799
800 # Aggiungi gene rule se presente
801 if pd.notna(row['Rule']) and str(row['Rule']).strip():
802 reaction.gene_reaction_rule = str(row['Rule']).strip()
803
804 # Parse della formula della reazione
805 try:
806 parse_reaction_formula(reaction, reaction_formula, metabolites_dict)
807 except Exception as e:
808 print(f"Errore nel parsing della reazione {reaction_id}: {e}")
809 reactions_skipped += 1
810 continue
811
812 # Aggiungi la reazione al modello
813 model.add_reactions([reaction])
814 reactions_added += 1
815
816 except Exception as e: 804 except Exception as e:
817 print(f"Errore nell'aggiungere la reazione {reaction_id}: {e}") 805 print(f"Errore nel parsing della reazione {reaction_id}: {e}")
818 reactions_skipped += 1 806 reactions_skipped += 1
819 continue 807 continue
808
809 # Aggiungi la reazione al modello
810 model.add_reactions([reaction])
811 reactions_added += 1
812
820 813
821 print(f"Aggiunte {reactions_added} reazioni, saltate {reactions_skipped} reazioni") 814 print(f"Aggiunte {reactions_added} reazioni, saltate {reactions_skipped} reazioni")
822 815
823 # Imposta l'obiettivo di biomassa 816 # Imposta l'obiettivo di biomassa
824 set_biomass_objective(model) 817 set_biomass_objective(model)