Source code for cobra.io.sbml

#cobra/sbml.py: Tools for reading / writing SBML now contained in
#this module
#System modules
from .. import Model, Reaction, Metabolite
from os.path import isfile
from os import name as __name
from warnings import warn
import re
from math import isnan, isinf

from six import iteritems

#
if __name == 'java':
    from org.sbml.jsbml import SBMLDocument, SpeciesReference, KineticLaw, Parameter
    from org.sbml.jsbml import SBMLReader, SBMLWriter
    __tmp_reader = SBMLReader()
    __tmp_writer = SBMLWriter()
    readSBML = __tmp_reader.readSBMLFromFile
    writeSBML = __tmp_writer.writeSBMLToFile
    from org.sbml.jsbml.Unit import Kind as __Kind
    UNIT_KIND_MOLE = __Kind.MOLE
    UNIT_KIND_GRAM = __Kind.GRAM
    UNIT_KIND_SECOND = __Kind.SECOND
    UNIT_KIND_DIMENSIONLESS = __Kind.DIMENSIONLESS
else:
    from libsbml import SBMLDocument, SpeciesReference, KineticLaw, Parameter
    from libsbml import readSBML, writeSBML
    from libsbml import UNIT_KIND_MOLE, UNIT_KIND_GRAM, UNIT_KIND_SECOND, UNIT_KIND_DIMENSIONLESS
[docs]def parse_legacy_id(the_id, the_compartment=None, the_type='metabolite', use_hyphens=False): """Deals with a bunch of problems due to bigg.ucsd.edu not following SBML standards the_id: String. the_compartment: String. the_type: String. Currently only 'metabolite' is supported use_hyphens: Boolean. If True, double underscores (__) in an SBML ID will be converted to hyphens """ if use_hyphens: the_id = the_id.replace('__','-') if the_type == 'metabolite': if the_id.split('_')[-1] == the_compartment: #Reformat Ids to match convention in Palsson Lab. the_id = the_id[:-len(the_compartment)-1] the_id += '[%s]'%the_compartment return the_id
[docs]def create_cobra_model_from_sbml_file(sbml_filename, old_sbml=False, legacy_metabolite=False, print_time=False, use_hyphens=False): """convert an SBML XML file into a cobra.Model object. Supports SBML Level 2 Versions 1 and 4. The function will detect if the SBML fbc package is used in the file and run the converter if the fbc package is used. sbml_filename: String. old_sbml: Boolean. Set to True if the XML file has metabolite formula appended to metabolite names. This was a poorly designed artifact that persists in some models. legacy_metabolite: Boolean. If True then assume that the metabolite id has the compartment id appended after an underscore (e.g. _c for cytosol). This has not been implemented but will be soon. print_time: deprecated use_hyphens: Boolean. If True, double underscores (__) in an SBML ID will be converted to hyphens """ __default_lower_bound = -1000 __default_upper_bound = 1000 __default_objective_coefficient = 0 # Ensure that the file exists if not isfile(sbml_filename): raise IOError('Your SBML file is not found: %s'%sbml_filename) #Expressions to change SBML Ids to Palsson Lab Ids metabolite_re = re.compile('^M_') reaction_re = re.compile('^R_') compartment_re = re.compile('^C_') if print_time: warn("print_time is deprecated") model_doc = readSBML(sbml_filename) if (model_doc.getPlugin("fbc") != None): from libsbml import ConversionProperties, LIBSBML_OPERATION_SUCCESS conversion_properties = ConversionProperties() conversion_properties.addOption("convert fbc to cobra", True, "Convert FBC model to Cobra model") result = model_doc.convert(conversion_properties) if result != LIBSBML_OPERATION_SUCCESS: raise(Exception("Conversion of SBML+fbc to COBRA failed")) sbml_model = model_doc.getModel() sbml_model_id = sbml_model.getId() sbml_species = sbml_model.getListOfSpecies() sbml_reactions = sbml_model.getListOfReactions() sbml_compartments = sbml_model.getListOfCompartments() compartment_dict = dict([(compartment_re.split(x.getId())[-1], x.getName()) for x in sbml_compartments]) if legacy_metabolite: #Deal with the palsson lab appending the compartment id to the metabolite id new_dict = {} for the_id, the_name in compartment_dict.items(): if the_name == '': new_dict[the_id[0].lower()] = the_id else: new_dict[the_id] = the_name compartment_dict = new_dict legacy_compartment_converter = dict([(v,k) for k, v in compartment_dict.items()]) cobra_model = Model(sbml_model_id) metabolites = [] metabolite_dict = {} #Convert sbml_metabolites to cobra.Metabolites for sbml_metabolite in sbml_species: #Skip sbml boundary species if sbml_metabolite.getBoundaryCondition(): continue if (old_sbml or legacy_metabolite) and \ sbml_metabolite.getId().endswith('_b'): #Deal with incorrect sbml from bigg.ucsd.edu continue tmp_metabolite = Metabolite() metabolite_id = tmp_metabolite.id = sbml_metabolite.getId() tmp_metabolite.compartment = compartment_re.split(sbml_metabolite.getCompartment())[-1] if legacy_metabolite: if tmp_metabolite.compartment not in compartment_dict: tmp_metabolite.compartment = legacy_compartment_converter[tmp_metabolite.compartment] tmp_metabolite.id = parse_legacy_id(tmp_metabolite.id, tmp_metabolite.compartment, use_hyphens=use_hyphens) if use_hyphens: tmp_metabolite.id = metabolite_re.split(tmp_metabolite.id)[-1].replace('__','-') else: #Just in case the SBML ids are ill-formed and use - tmp_metabolite.id = metabolite_re.split(tmp_metabolite.id)[-1].replace('-','__') tmp_metabolite.name = sbml_metabolite.getName() tmp_formula = '' tmp_metabolite.notes = parse_legacy_sbml_notes(sbml_metabolite.getNotesString()) if sbml_metabolite.isSetCharge(): tmp_metabolite.charge = sbml_metabolite.getCharge() if "CHARGE" in tmp_metabolite.notes: note_charge = tmp_metabolite.notes["CHARGE"][0] try: note_charge = float(note_charge) if note_charge == int(note_charge): note_charge = int(note_charge) except: warn("charge of %s is not a number (%s)" % (tmp_metabolite.id, str(note_charge))) else: if tmp_metabolite.charge is None or tmp_metabolite.charge == note_charge: tmp_metabolite.notes.pop("CHARGE") else: # tmp_metabolite.charge != note_charge msg = "different charges specified for %s (%d and %d)" msg = msg % (tmp_metabolite.id, tmp_metabolite.charge, note_charge) warn(msg) # Chances are a 0 note charge was written by mistake. We # will default to the note_charge in this case. if tmp_metabolite.charge == 0: tmp_metabolite.charge = note_charge for the_key in tmp_metabolite.notes.keys(): if the_key.lower() == 'formula': tmp_formula = tmp_metabolite.notes.pop(the_key)[0] break if tmp_formula == '' and old_sbml: tmp_formula = tmp_metabolite.name.split('_')[-1] tmp_metabolite.name = tmp_metabolite.name[:-len(tmp_formula)-1] tmp_metabolite.formula = tmp_formula metabolite_dict.update({metabolite_id: tmp_metabolite}) metabolites.append(tmp_metabolite) cobra_model.add_metabolites(metabolites) #Construct the vectors and matrices for holding connectivity and numerical info #to feed to the cobra toolbox. #Always assume steady state simulations so b is set to 0 cobra_reaction_list = [] for sbml_reaction in sbml_reactions: if use_hyphens: #Change the ids to match conventions used by the Palsson lab. reaction = Reaction(reaction_re.split(sbml_reaction.getId())[-1].replace('__','-')) else: #Just in case the SBML ids are ill-formed and use - reaction = Reaction(reaction_re.split(sbml_reaction.getId())[-1].replace('-','__')) cobra_reaction_list.append(reaction) #reaction.exchange_reaction = 0 reaction.name = sbml_reaction.getName() cobra_metabolites = {} #Use the cobra.Metabolite class here for sbml_metabolite in sbml_reaction.getListOfReactants(): tmp_metabolite_id = sbml_metabolite.getSpecies() #This deals with boundary metabolites if tmp_metabolite_id in metabolite_dict: tmp_metabolite = metabolite_dict[tmp_metabolite_id] cobra_metabolites[tmp_metabolite] = -sbml_metabolite.getStoichiometry() for sbml_metabolite in sbml_reaction.getListOfProducts(): tmp_metabolite_id = sbml_metabolite.getSpecies() #This deals with boundary metabolites if tmp_metabolite_id in metabolite_dict: tmp_metabolite = metabolite_dict[tmp_metabolite_id] # Handle the case where the metabolite was specified both # as a reactant and as a product. if tmp_metabolite in cobra_metabolites: warn("%s appears as a reactant and product %s" % (tmp_metabolite_id, reaction.id)) cobra_metabolites[tmp_metabolite] += sbml_metabolite.getStoichiometry() # if the combined stoichiometry is 0, remove the metabolite if cobra_metabolites[tmp_metabolite] == 0: cobra_metabolites.pop(tmp_metabolite) else: cobra_metabolites[tmp_metabolite] = sbml_metabolite.getStoichiometry() # check for nan for met, v in iteritems(cobra_metabolites): if isnan(v) or isinf(v): warn("invalid value %s for metabolite '%s' in reaction '%s'" % (str(v), met.id, reaction.id)) reaction.add_metabolites(cobra_metabolites) #Parse the kinetic law info here. parameter_dict = {} #If lower and upper bounds are specified in the Kinetic Law then #they override the sbml reversible attribute. If they are not #specified then the bounds are determined by getReversible. if not sbml_reaction.getKineticLaw(): if sbml_reaction.getReversible(): parameter_dict['lower_bound'] = __default_lower_bound parameter_dict['upper_bound'] = __default_upper_bound else: #Assume that irreversible reactions only proceed from left to right. parameter_dict['lower_bound'] = 0 parameter_dict['upper_bound'] = __default_upper_bound parameter_dict['objective_coefficient'] = __default_objective_coefficient else: for sbml_parameter in sbml_reaction.getKineticLaw().getListOfParameters(): parameter_dict[sbml_parameter.getId().lower()] = sbml_parameter.getValue() if 'lower_bound' in parameter_dict: reaction.lower_bound = parameter_dict['lower_bound'] elif 'lower bound' in parameter_dict: reaction.lower_bound = parameter_dict['lower bound'] elif sbml_reaction.getReversible(): reaction.lower_bound = __default_lower_bound else: reaction.lower_bound = 0 if 'upper_bound' in parameter_dict: reaction.upper_bound = parameter_dict['upper_bound'] elif 'upper bound' in parameter_dict: reaction.upper_bound = parameter_dict['upper bound'] else: reaction.upper_bound = __default_upper_bound if 'objective_coefficient' in parameter_dict: reaction.objective_coefficient = parameter_dict['objective_coefficient'] elif 'objective coefficient' in parameter_dict: reaction.objective_coefficient = parameter_dict['objective coefficient'] else: reaction.objective_coefficient = __default_objective_coefficient # ensure values are not set to nan or inf if isnan(reaction.lower_bound) or isinf(reaction.lower_bound): reaction.lower_bound = __default_lower_bound if isnan(reaction.upper_bound) or isinf(reaction.upper_bound): reaction.upper_bound = __default_upper_bound reaction_note_dict = parse_legacy_sbml_notes(sbml_reaction.getNotesString()) #Parse the reaction notes. #POTENTIAL BUG: DEALING WITH LEGACY 'SBML' THAT IS NOT IN A #STANDARD FORMAT #TODO: READ IN OTHER NOTES AND GIVE THEM A reaction_ prefix. #TODO: Make sure genes get added as objects if 'GENE ASSOCIATION' in reaction_note_dict: rule = reaction_note_dict['GENE ASSOCIATION'][0] try: rule.encode('ascii') except (UnicodeEncodeError, UnicodeDecodeError): warn("gene_reaction_rule '%s' is not ascii compliant" % rule) if rule.startswith(""") and rule.endswith("""): rule = rule[6:-6] reaction.gene_reaction_rule = rule if 'GENE LIST' in reaction_note_dict: reaction.systematic_names = reaction_note_dict['GENE LIST'][0] elif 'GENES' in reaction_note_dict and \ reaction_note_dict['GENES'] != ['']: reaction.systematic_names = reaction_note_dict['GENES'][0] elif 'LOCUS' in reaction_note_dict: gene_id_to_object = dict([(x.id, x) for x in reaction._genes]) for the_row in reaction_note_dict['LOCUS']: tmp_row_dict = {} the_row = 'LOCUS:' + the_row.lstrip('_').rstrip('#') for the_item in the_row.split('#'): k, v = the_item.split(':') tmp_row_dict[k] = v tmp_locus_id = tmp_row_dict['LOCUS'] if 'TRANSCRIPT' in tmp_row_dict: tmp_locus_id = tmp_locus_id + '.' + tmp_row_dict['TRANSCRIPT'] if 'ABBREVIATION' in tmp_row_dict: gene_id_to_object[tmp_locus_id].name = tmp_row_dict['ABBREVIATION'] if 'SUBSYSTEM' in reaction_note_dict: reaction.subsystem = reaction_note_dict.pop('SUBSYSTEM')[0] reaction.notes = reaction_note_dict #Now, add all of the reactions to the model. cobra_model.id = sbml_model.getId() #Populate the compartment list - This will be done based on cobra.Metabolites #in cobra.Reactions in the future. cobra_model.compartments = compartment_dict cobra_model.add_reactions(cobra_reaction_list) #cobra_model.update_rules() return cobra_model
[docs]def parse_legacy_sbml_notes(note_string, note_delimiter = ':'): """Deal with legacy SBML format issues arising from the COBRA Toolbox for MATLAB and BiGG.ucsd.edu developers. """ note_dict = {} start_tag = '<p>' end_tag = '</p>' if '<html:p>' in note_string: start_tag = '<html:p>' end_tag = '</html:p>' while start_tag in note_string and end_tag in note_string: note_start = note_string.index(start_tag) note_end = note_string.index(end_tag) the_note = note_string[(note_start + len(start_tag)):note_end].lstrip(' ').rstrip(' ') if note_delimiter in the_note: note_delimiter_index = the_note.index(note_delimiter) note_field = the_note[:note_delimiter_index].lstrip(' ').rstrip(' ').replace('_',' ').upper() note_value = the_note[(note_delimiter_index+1):].lstrip(' ').rstrip(' ') if note_field in note_dict: note_dict[note_field].append(note_value) else: note_dict[note_field] = [note_value] note_string = note_string[(note_end+len(end_tag)): ] if 'CHARGE' in note_dict and note_dict['CHARGE'][0].lower() in ['none', 'na', 'nan']: note_dict.pop('CHARGE') #Remove non-numeric charges return(note_dict)
[docs]def write_cobra_model_to_sbml_file(cobra_model, sbml_filename, sbml_level=2, sbml_version=1, print_time=False, use_fbc_package=True): """Write a cobra.Model object to an SBML XML file. cobra_model: :class:`~cobra.core.Model.Model` object sbml_filename: The file to write the SBML XML to. sbml_level: 2 is the only level supported at the moment. sbml_version: 1 is the only version supported at the moment. use_fbc_package: Boolean. Convert the model to the FBC package format to improve portability. http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/Flux_Balance_Constraints_(flux) TODO: Update the NOTES to match the SBML standard and provide support for Level 2 Version 4 """ sbml_doc = get_libsbml_document(cobra_model, sbml_level=sbml_level, sbml_version=sbml_version, print_time=print_time, use_fbc_package=use_fbc_package) writeSBML(sbml_doc, sbml_filename)
[docs]def get_libsbml_document(cobra_model, sbml_level=2, sbml_version=1, print_time=False, use_fbc_package=True): """ Return a libsbml document object for writing to a file. This function is used by write_cobra_model_to_sbml_file(). """ note_start_tag, note_end_tag = '<p>', '</p>' if sbml_level > 2 or (sbml_level == 2 and sbml_version == 4): note_start_tag, note_end_tag = '<html:p>', '</html:p>' sbml_doc = SBMLDocument(sbml_level, sbml_version) sbml_model = sbml_doc.createModel(cobra_model.id.split('.')[0]) #Note need to set units reaction_units = 'mmol_per_gDW_per_hr' model_units = sbml_model.createUnitDefinition() model_units.setId(reaction_units) sbml_unit = model_units.createUnit() sbml_unit.setKind(UNIT_KIND_MOLE) sbml_unit.setScale(-3) sbml_unit = model_units.createUnit() sbml_unit.setKind(UNIT_KIND_GRAM) sbml_unit.setExponent(-1) sbml_unit = model_units.createUnit() sbml_unit.setKind(UNIT_KIND_SECOND) sbml_unit.setMultiplier(1.0/60/60) sbml_unit.setExponent(-1) #Add in the common compartment abbreviations. If there are additional compartments #they also need to be added. if not cobra_model.compartments: cobra_model.compartments = {'c': 'cytosol', 'p': 'periplasm', 'e': 'extracellular'} for the_key in cobra_model.compartments.keys(): sbml_comp = sbml_model.createCompartment() sbml_comp.setId(the_key) sbml_comp.setName(cobra_model.compartments[the_key]) sbml_comp.setSize(1) #Just to get rid of warnings if print_time: warn("print_time is deprecated") #Use this dict to allow for fast look up of species id #for references created in the reaction section. metabolite_dict = {} for cobra_metabolite in cobra_model.metabolites: metabolite_dict[cobra_metabolite.id] = add_sbml_species(sbml_model, cobra_metabolite, note_start_tag=note_start_tag, note_end_tag=note_end_tag) for the_reaction in cobra_model.reactions: #This is probably the culprit. Including cobra.Reaction #objects explicitly in cobra.Model will speed this up. sbml_reaction = sbml_model.createReaction() #Need to remove - for proper SBML. Replace with __ the_reaction_id = 'R_' + the_reaction.id.replace('-','__' ) sbml_reaction.setId(the_reaction_id) # The reason we are not using the Reaction.reversibility property # is because the SBML definition of reversibility does not quite # match with the cobra definition. In cobra, reversibility implies # that both positive and negative flux values are feasible. However, # SBML requires negative-flux-only reactions to still be classified # as reversible. To quote from the SBML Level 3 Version 1 Spec: # > However, labeling a reaction as irreversible is interpreted as # > an assertion that the rate expression will not have negative # > values during a simulation. # (Page 60 lines 44-45) sbml_reaction.setReversible(the_reaction.lower_bound < 0) if the_reaction.name: sbml_reaction.setName(the_reaction.name) else: sbml_reaction.setName(the_reaction.id) #Add in the reactant/product references for the_metabolite, the_coefficient in the_reaction._metabolites.items(): sbml_stoichiometry = the_coefficient metabolite_id = str(metabolite_dict[the_metabolite.id]) #Each SpeciesReference must have a unique id if sbml_stoichiometry < 0: species_reference = sbml_reaction.createReactant() else: species_reference = sbml_reaction.createProduct() species_reference.setId(metabolite_id + '_' + the_reaction_id) species_reference.setSpecies(metabolite_id) species_reference.setStoichiometry(abs(sbml_stoichiometry)) #Deal with the case where the reaction is a boundary reaction if len(the_reaction._metabolites) == 1: the_metabolite, the_coefficient = list(the_reaction._metabolites.items())[0] metabolite_id = add_sbml_species(sbml_model, the_metabolite, note_start_tag=note_start_tag, note_end_tag=note_end_tag, boundary_metabolite=True) sbml_stoichiometry = -the_coefficient #Each SpeciesReference must have a unique id if sbml_stoichiometry < 0: species_reference = sbml_reaction.createReactant() else: species_reference = sbml_reaction.createProduct() species_reference.setId(metabolite_id + '_' + the_reaction_id) species_reference.setSpecies(metabolite_id) species_reference.setStoichiometry(abs(sbml_stoichiometry)) #Add in the kineticLaw sbml_law = KineticLaw(sbml_level, sbml_version) if hasattr(sbml_law, 'setId'): sbml_law.setId('FLUX_VALUE') sbml_law.setFormula('FLUX_VALUE') reaction_parameter_dict = {'LOWER_BOUND': [the_reaction.lower_bound, reaction_units], 'UPPER_BOUND': [the_reaction.upper_bound, reaction_units], 'FLUX_VALUE': [0, reaction_units], 'OBJECTIVE_COEFFICIENT': [the_reaction.objective_coefficient, 'dimensionless']} for k, v in reaction_parameter_dict.items(): sbml_parameter = Parameter(sbml_level, sbml_version) sbml_parameter.setId(k) if hasattr(v, '__iter__'): sbml_parameter.setValue(v[0]) sbml_parameter.setUnits(v[1]) else: sbml_parameter.setValue(v) sbml_law.addParameter(sbml_parameter) sbml_reaction.setKineticLaw(sbml_law) #Checks if GPR and Subsystem annotations are present in the notes section and if they are the same as those in #the reaction's gene_reaction_rule/ subsystem attribute #If they are not identical, they are set to be identical note_dict = the_reaction.notes.copy() if the_reaction.gene_reaction_rule: note_dict['GENE_ASSOCIATION'] = [str(the_reaction.gene_reaction_rule)] if the_reaction.subsystem: note_dict['SUBSYSTEM'] = [str(the_reaction.subsystem)] #In a cobrapy model the notes section is stored as a dictionary. The following section turns the key-value-pairs #of the dictionary into a string and replaces recurring symbols so that the string has the required syntax for #an SBML doc. note_str = str(list(iteritems(note_dict))) note_start_tag, note_end_tag, note_delimiter = '<p>', '</p>', ':' note_str = note_str.replace('(\'',note_start_tag) note_str = note_str.replace('\']),',note_end_tag) note_str = note_str.replace('\',',note_delimiter) note_str = note_str.replace('\']','') note_str = note_str.replace('[\'','') note_str = note_str.replace('[','<html xmlns="http://www.w3.org/1999/xhtml">') note_str = note_str.replace(')]',note_end_tag+'</html>') sbml_reaction.setNotes(note_str) if use_fbc_package: try: from libsbml import ConversionProperties, LIBSBML_OPERATION_SUCCESS conversion_properties = ConversionProperties() conversion_properties.addOption("convert cobra", True, "Convert Cobra model") result = sbml_doc.convert(conversion_properties) if result != LIBSBML_OPERATION_SUCCESS: raise Exception("Conversion of COBRA to SBML+fbc failed") except Exception as e: error_string = 'Error saving as SBML+fbc. %s' try: #Check whether the FbcExtension is there from libsbml import FbcExtension error_string = error_string%e except ImportError: error_string = error_string%'FbcExtension not available in libsbml. ' +\ 'If use_fbc_package == True then libsbml must be compiled with ' +\ 'the fbc extension. ' from libsbml import getLibSBMLDottedVersion _sbml_version = getLibSBMLDottedVersion() _major, _minor, _patch = map(int, _sbml_version.split('.')) if _major < 5 or (_major == 5 and _minor < 8): error_string += "You've got libsbml %s installed. You need 5.8.0 or later with the fbc package" raise(Exception(error_string)) return sbml_doc
[docs]def add_sbml_species(sbml_model, cobra_metabolite, note_start_tag, note_end_tag, boundary_metabolite=False): """A helper function for adding cobra metabolites to an sbml model. sbml_model: sbml_model object cobra_metabolite: a cobra.Metabolite object note_start_tag: the start tag for parsing cobra notes. this will eventually be supplanted when COBRA is worked into sbml. note_end_tag: the end tag for parsing cobra notes. this will eventually be supplanted when COBRA is worked into sbml. """ sbml_species = sbml_model.createSpecies() the_id = 'M_' + cobra_metabolite.id.replace('-', '__') #Deal with legacy naming issues the_compartment = cobra_metabolite.compartment if the_id.endswith('[%s]'%the_compartment): the_id = the_id[:-len('[%s]'%the_compartment)] elif not the_id.endswith('_%s'%the_compartment): the_id += '_%s'%the_compartment if boundary_metabolite: the_id += '_boundary' sbml_species.setId(the_id) metabolite_id = the_id if boundary_metabolite: sbml_species.setBoundaryCondition(True) if cobra_metabolite.name: sbml_species.setName(cobra_metabolite.name) else: sbml_species.setName(cobra_metabolite.id) if the_compartment is not None: try: sbml_species.setCompartment(the_compartment) except: warn('metabolite failed: ' + the_id) return cobra_metabolite if cobra_metabolite.charge is not None: sbml_species.setCharge(cobra_metabolite.charge) #Deal with cases where the formula in the model is not an object but as a string if cobra_metabolite.formula or cobra_metabolite.notes: tmp_note = '<html xmlns="http://www.w3.org/1999/xhtml">' if hasattr(cobra_metabolite.formula, 'id'): tmp_note += '%sFORMULA: %s%s'%(note_start_tag, cobra_metabolite.formula.id, note_end_tag) else: tmp_note += '%sFORMULA: %s%s'%(note_start_tag, cobra_metabolite.formula, note_end_tag) if hasattr(cobra_metabolite.notes, 'items'): for the_id_type, the_id in cobra_metabolite.notes.items(): if the_id_type.lower() == 'charge': continue #Use of notes['CHARGE'] has been deprecated in favor of metabolite.charge if not isinstance(the_id_type, str): the_id_type = str(the_id_type) if hasattr(the_id, '__iter__') and len(the_id) == 1: the_id = the_id[0] if not isinstance(the_id, str): the_id = str(the_id) tmp_note += '%s%s: %s%s'%(note_start_tag, the_id_type, the_id, note_end_tag) sbml_species.setNotes(tmp_note + '</html>') return metabolite_id
[docs]def fix_legacy_id(id, use_hyphens=False, fix_compartments=False): id = id.replace('_DASH_', '__') id = id.replace('_FSLASH_', '/') id = id.replace('_BSLASH_', "\\") id = id.replace('_LPAREN_', '(') id = id.replace('_LSQBKT_', '[') id = id.replace('_RSQBKT_', ']') id = id.replace('_RPAREN_', ')') id = id.replace('_COMMA_', ',') id = id.replace('_PERIOD_', '.') id = id.replace('_APOS_', "'") id = id.replace('&amp;', '&') id = id.replace('&lt;', '<') id = id.replace('&gt;', '>') id = id.replace('&quot;', '"') if use_hyphens: id = id.replace('__', '-') else: id = id.replace("-", "__") if fix_compartments: if len(id) > 2: if (id[-3] == "(" and id[-1] == ")") or \ (id[-3] == "[" and id[-1] == "]"): id = id[:-3] + "_" + id[-2] return id
[docs]def read_legacy_sbml(filename, use_hyphens=False): """read in an sbml file and fix the sbml id's""" model = create_cobra_model_from_sbml_file(filename, old_sbml=True) for metabolite in model.metabolites: metabolite.id = fix_legacy_id(metabolite.id) model.metabolites._generate_index() for reaction in model.reactions: reaction.id = fix_legacy_id(reaction.id) if reaction.id.startswith("EX_") and reaction.id.endswith("(e)"): reaction.id = reaction.id[:-3] + "_e" model.reactions._generate_index() # remove boundary metabolites (end in _b and only present in exchanges) for metabolite in list(model.metabolites): if not metabolite.id.endswith("_b"): continue if len(metabolite._reaction) == 1: if list(metabolite._reaction)[0].id.startswith("EX_"): metabolite.remove_from_model() model.metabolites._generate_index() return model