cobraxy: COBRAxy/utils/model_utils.py comparison

comparison COBRAxy/utils/model_utils.py @ 501:9bfd1ec3ae6f draft

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author	francesco_lapi
date	Tue, 30 Sep 2025 17:06:37 +0000
parents	4e7e67693ce7
children	8dd07e59f631

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-:4e7e67693ce7
+:9bfd1ec3ae6f
 Returns:
 cobra.Model: The constructed COBRApy model.
 """
-df = pd.read_csv(csv_path, sep='\t')
+# Try to detect separator
+with open(csv_path, 'r') as f:
+first_line = f.readline()
+sep = '\t' if '\t' in first_line else ','
+df = pd.read_csv(csv_path, sep=sep)
+# Check required columns
+required_cols = ['ReactionID', 'Formula']
+missing_cols = [col for col in required_cols if col not in df.columns]
+if missing_cols:
+raise ValueError(f"Missing required columns: {missing_cols}. Available columns: {list(df.columns)}")
 model = cobraModel(model_id)
 metabolites_dict = {}
 compartments_dict = {}
 Returns the IDs including the compartment suffix exactly as written.
 """
 pattern = re.compile(
 r'(?:^|(?<=\s)|(?<=\+)|(?<=,)|(?<==)|(?<=:))'              # left boundary (start, space, +, comma, =, :)
-r'(?:\d+(?:\.\d+)?\s*)?'                                   # optional coefficient
+r'(?:\d+(?:\.\d+)?\s+)?'                                   # optional coefficient (requires space after)
-r'([A-Za-z0-9_]+(?:\[[A-Za-z0-9]+\]|_[A-Za-z0-9]+))'       # metabolite + compartment
+r'([A-Za-z0-9][A-Za-z0-9_]*(?:\[[A-Za-z0-9]+\]|_[A-Za-z0-9]+))'  # metabolite + compartment (can start with number)
 )
 return {m.group(1) for m in pattern.finditer(reaction_formula)}
 def parse_reaction_formula(reaction: Reaction, formula: str, metabolites_dict: Dict[str, Metabolite]):
 """Parse a reaction formula and set metabolites with their coefficients."""
 if '<=>' in formula:
-left, right = formula.split('<=>')
+parts = formula.split('<=>')
 reversible = True
 elif '<--' in formula:
-left, right = formula.split('<--')
+parts = formula.split('<--')
 reversible = False
 elif '-->' in formula:
-left, right = formula.split('-->')
+parts = formula.split('-->')
 reversible = False
 elif '<-' in formula:
-left, right = formula.split('<-')
+parts = formula.split('<-')
 reversible = False
 else:
 raise ValueError(f"Unrecognized reaction format: {formula}")
-reactants = parse_metabolites_side(left.strip())
+# Handle cases where one side might be empty (exchange reactions)
-products = parse_metabolites_side(right.strip())
+if len(parts) != 2:
+raise ValueError(f"Invalid reaction format, expected 2 parts: {formula}")
+left, right = parts[0].strip(), parts[1].strip()
+reactants = parse_metabolites_side(left) if left else {}
+products = parse_metabolites_side(right) if right else {}
 metabolites_to_add = {}
 for met_id, coeff in reactants.items():
 if met_id in metabolites_dict:
 for term in terms:
 term = term.strip()
 if not term:
 continue
-# optional coefficient + id ending with _<compartment>
+# First check if term has space-separated coefficient and metabolite
-match = re.match(r'(?:(\d+\.?\d*)\s+)?([A-Za-z0-9_]+_[a-z]+)', term)
+parts = term.split()
-if match:
+if len(parts) == 2:
-coeff_str, met_id = match.groups()
+# Two parts: potential coefficient + metabolite
-coeff = float(coeff_str) if coeff_str else 1.0
+try:
-metabolites[met_id] = coeff
+coeff = float(parts[0])
+met_id = parts[1]
+# Verify the second part looks like a metabolite with compartment
+if re.match(r'[A-Za-z0-9_]+(?:\[[A-Za-z0-9]+\]|_[A-Za-z0-9]+)', met_id):
+metabolites[met_id] = coeff
+continue
+except ValueError:
+pass
+# Single term - check if it's a metabolite (no coefficient)
+# Updated pattern to include metabolites starting with numbers
+if re.match(r'[A-Za-z0-9][A-Za-z0-9_]*(?:\[[A-Za-z0-9]+\]|_[A-Za-z0-9]+)', term):
+metabolites[term] = 1.0
+else:
+print(f"Warning: Could not parse metabolite term: '{term}'")
 return metabolites
 def set_medium_from_data(model: cobraModel, df: pd.DataFrame):
 """Set the medium based on the 'InMedium' column in the dataframe."""
+if 'InMedium' not in df.columns:
+print("No 'InMedium' column found, skipping medium setup")
+return
 medium_reactions = df[df['InMedium'] == True]['ReactionID'].tolist()
 medium_dict = {}
 for rxn_id in medium_reactions:
 if rxn_id in [r.id for r in model.reactions]:
 reaction = model.reactions.get_by_id(rxn_id)
-if reaction.lower_bound < 0:  # Solo reazioni di uptake
+if reaction.lower_bound < 0:
 medium_dict[rxn_id] = abs(reaction.lower_bound)
 if medium_dict:
 model.medium = medium_dict
 print(f"Medium set with {len(medium_dict)} components")
+else:
+print("No medium components found")
 def validate_model(model: cobraModel) -> Dict[str, any]:
 """Validate the model and return basic statistics."""
 validation = {
 'num_reactions': len(model.reactions),
 'num_metabolites': len(model.metabolites),

Mercurial > repos > bimib > cobraxy

comparison COBRAxy/utils/model_utils.py @ 501:9bfd1ec3ae6f draft