Created entities.py #52

refinegems/entities.py

@@ -0,0 +1,98 @@
+#!/usr/bin/env python
+from Bio import Entrez, SeqIO
+from refinegems.cvterms import add_cv_term_genes, add_cv_term_metabolites, add_cv_term_reactions
+
+
+def get_name_from_locus(locus):
+    """fetches protein name from NCBI
+
+    Args:
+        locus (string): NCBI compatible locus_tag
+
+    Returns:
+        str: protein name / description
+    """
+    handle = Entrez.efetch(
+        db="protein",
+        id=locus,
+        rettype="gbwithparts",
+        retmode='text')
+    records = SeqIO.parse(handle, "gb")
+
+    for i, record in enumerate(records):
+        return record.description
+
+
+def create_gpr(model, locus_tag, email):
+    """creates GeneProduct in the given model
+
+    Args:
+        model (libsbml-model): model loaded with libSBML
+        locus_tag (string): NCBI compatible locus_tag
+        email (string): User Email to access the NCBI Entrez database
+
+    Returns:
+        tuple: (gpr, modified model)
+    """
+    Entrez.email = email
+    gpr = model.getPlugin(0).createGeneProduct()
+    name = get_name_from_locus(locus_tag)
+    gpr.setName(name)
+    gpr.setId(locus_tag)
+    gpr.setMetaId('meta_' + locus_tag)
+    gpr.setLabel(locus_tag)
+    gpr.setSBOTerm("SBO:0000243")
+    add_cv_term_genes(locus_tag, 'NCBI', gpr)
+    return gpr, model
+
+
+def create_reaction(model, reaction_id, name, reactants, products, fluxes, reversible, fast, sbo):
+    """creates new reaction in the given model
+
+    Args:
+        model (libsbml-model): model loaded with libSBML
+        reaction_id (str): BiGG id of the reaction to create
+        name (string): human readable name of the reaction
+        reactants (dict): metabolites as keys and their stoichiometry as values
+        products (dict): metabolites as keys and their stoichiometry as values
+        fluxes (dict): lower_bound and upper_bound as keys
+        reversible (bool): true/false for the reaction
+        fast (bool): true/false for the reaction
+        sbo (string): SBO term of the reaction
+
+    Returns:
+        tuple: (reaction, modified model)
+    """
+    reaction = model.createReaction()
+    reaction.setId('R_' + reaction_id)
+    reaction.setName(name)
+    reaction.setMetaId('meta_R_' + reaction_id)
+    reaction.setSBOTerm(sbo)
+    reaction.setFast(fast)
+    reaction.setReversible(reversible)
+    for metab, stoich in reactants.items(): #reactants as dict with metab:stoich
+        reaction.addReactant(model.getSpecies('M_' + metab), stoich)
+    for metab, stoich in products.items(): #reactants as dict with metab:stoich
+        reaction.addProduct(model.getSpecies('M_' + metab), stoich)
+    reaction.getPlugin(0).setLowerFluxBound(fluxes['lower_bound'])
+    reaction.getPlugin(0).setUpperFluxBound(fluxes['upper_bound'])
+    add_cv_term_reactions(reaction_id, 'BIGG', reaction)
+    return reaction, model
+
+
+def create_species(model: Model, metabolite_id: str, name: str, compartment_id: str):
+   metabolite = model.createSpecies()
+   metabolite.setId(f'M_{metabolite_id}')
+   metabolite.setName(name)
+   metabolite.setMetaId(f'meta_M_{metabolite_id}')
+   metabolite.setSBOTerm('SBO:0000247')
+   metabolite.setInitialAmount(float('NaN'))
+   metabolite.setHasOnlySubstanceUnits(True)
+   metabolite.setBoundaryCondition(False)
+   metabolite.setConstant(False)
+   metabolite.setCompartment(compartment_id)
+   metabolite.setCharge(0)  # Reihaneh set charges to 0 as not provided by BioCyc
+   metabolite.setChemicalFormula()
+   metabolite.enablePackage()
+   add_cv_term_metabolites(metabolite_id, 'BIGG', metabolite)
+