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

Uploaded

411:6b015d3184ab

import zipfile
import gzip
import bz2
from io import StringIO
import rule_parsing  as rulesUtils
import reaction_parsing as reactionUtils



class ValueErr(Exception):
    def __init__(self, param_name, expected, actual):

    
    print(f"Aggiunti {len(metabolites_dict)} metaboliti e {len(compartments_dict)} compartimenti")
    
    # Seconda passata: aggiungi le reazioni
    reactions_added = 0
    reactions_skipped = 0
    
    for idx, row in df.iterrows():
        try:
            reaction_id = str(row['ReactionID']).strip()
            reaction_formula = str(row['Reaction']).strip()
            
            # Salta reazioni senza formula
            if not reaction_formula or reaction_formula == 'nan':
                reactions_skipped += 1
                continue
            
            # Crea la reazione
            reaction = Reaction(reaction_id)
            reaction.name = reaction_id
            
            # Imposta bounds
            reaction.lower_bound = float(row['lower_bound']) if pd.notna(row['lower_bound']) else -1000.0
            reaction.upper_bound = float(row['upper_bound']) if pd.notna(row['upper_bound']) else 1000.0
            
            # Aggiungi gene rule se presente
            if pd.notna(row['Rule']) and str(row['Rule']).strip():
                reaction.gene_reaction_rule = str(row['Rule']).strip()
            
            # Parse della formula della reazione
            try:
                parse_reaction_formula(reaction, reaction_formula, metabolites_dict)
            except Exception as e:
                print(f"Errore nel parsing della reazione {reaction_id}: {e}")
                reactions_skipped += 1
                continue
            
            # Aggiungi la reazione al modello
            model.add_reactions([reaction])
            reactions_added += 1
            
        except Exception as e:
            print(f"Errore nell'aggiungere la reazione {reaction_id}: {e}")
            reactions_skipped += 1
            continue
    
    print(f"Aggiunte {reactions_added} reazioni, saltate {reactions_skipped} reazioni")
    
    # Imposta l'obiettivo di biomassa
    set_biomass_objective(model)

412:bdf4630ac1eb

import zipfile
import gzip
import bz2
from io import StringIO
import utils.rule_parsing  as rulesUtils
import utils.reaction_parsing as reactionUtils



class ValueErr(Exception):
    def __init__(self, param_name, expected, actual):

    
    print(f"Aggiunti {len(metabolites_dict)} metaboliti e {len(compartments_dict)} compartimenti")
    
    # Seconda passata: aggiungi le reazioni
    reactions_added = 0
    
    for idx, row in df.iterrows():
        reaction_id = str(row['ReactionID']).strip()
        reaction_formula = str(row['Reaction']).strip()
        
        # Salta reazioni senza formula
        if not reaction_formula or reaction_formula == 'nan':
            raise ValueError(f"Formula della reazione mancante {reaction_id}")

        # Crea la reazione
        reaction = Reaction(reaction_id)
        reaction.name = reaction_id
        
        # Imposta bounds
        reaction.lower_bound = float(row['lower_bound']) if pd.notna(row['lower_bound']) else -1000.0
        reaction.upper_bound = float(row['upper_bound']) if pd.notna(row['upper_bound']) else 1000.0
        
        # Aggiungi gene rule se presente
        if pd.notna(row['Rule']) and str(row['Rule']).strip():
            reaction.gene_reaction_rule = str(row['Rule']).strip()
        
        # Parse della formula della reazione
        try:
            parse_reaction_formula(reaction, reaction_formula, metabolites_dict)
        except Exception as e:
            print(f"Errore nel parsing della reazione {reaction_id}: {e}")
            reactions_skipped += 1
            continue
        
        # Aggiungi la reazione al modello
        model.add_reactions([reaction])
        reactions_added += 1
            
    
    print(f"Aggiunte {reactions_added} reazioni, saltate {reactions_skipped} reazioni")
    
    # Imposta l'obiettivo di biomassa
    set_biomass_objective(model)