Source code for

from collections import defaultdict
from warnings import warn, catch_warnings, simplefilter
from decimal import Decimal
from ast import Name, Or, And, BoolOp
from gzip import GzipFile
from bz2 import BZ2File
from tempfile import NamedTemporaryFile
from sys import exc_info
import re

from six import iteritems, string_types

from .. import Metabolite, Reaction, Gene, Model
from ..core.Gene import parse_gpr
from ..manipulation.modify import _renames
from ..manipulation.validate import check_reaction_bounds, \

    from lxml.etree import parse, Element, SubElement, \
        ElementTree, register_namespace, ParseError, XPath
    _with_lxml = True
except ImportError:
    warn("Install lxml for faster SBML I/O")
    _with_lxml = False
        from xml.etree.cElementTree import parse, Element, SubElement, \
            ElementTree, register_namespace, ParseError
    except ImportError:
        from xml.etree.ElementTree import parse, Element, SubElement, \
            ElementTree, register_namespace, ParseError

# use sbml level 2 from (which uses libsbml). Eventually, it would
# be nice to use the libSBML converters directly instead.
    import libsbml
except ImportError:
    libsbml = None
    from .sbml import create_cobra_model_from_sbml_file as read_sbml2
    from .sbml import write_cobra_model_to_sbml_file as write_sbml2

    from sympy import Basic
[docs] class Basic: pass
# deal with namespaces namespaces = {"fbc": "", "sbml": "", "rdf": "", "bqbiol": ""} for key in namespaces: register_namespace(key, namespaces[key])
[docs]def ns(query): """replace prefixes with namespace""" for prefix, uri in iteritems(namespaces): query = query.replace(prefix + ":", "{" + uri + "}") return query
# XPATH query wrappers fbc_prefix = "{" + namespaces["fbc"] + "}" sbml_prefix = "{" + namespaces["sbml"] + "}" SBML_DOT = "__SBML_DOT__" # FBC TAGS OR_TAG = ns("fbc:or") AND_TAG = ns("fbc:and") GENEREF_TAG = ns("fbc:geneProductRef") GPR_TAG = ns("fbc:geneProductAssociation") GENELIST_TAG = ns("fbc:listOfGeneProducts") GENE_TAG = ns("fbc:geneProduct") # XPATHS BOUND_XPATH = ns("sbml:listOfParameters/sbml:parameter[@value]") COMPARTMENT_XPATH = ns("sbml:listOfCompartments/sbml:compartment") GENES_XPATH = GENELIST_TAG + "/" + GENE_TAG SPECIES_XPATH = ns("sbml:listOfSpecies/sbml:species[@boundaryCondition='%s']") OBJECTIVES_XPATH = ns("fbc:objective[@fbc:id='%s']/" "fbc:listOfFluxObjectives/" "fbc:fluxObjective") if _with_lxml: RDF_ANNOTATION_XPATH = ("sbml:annotation/rdf:RDF/" "rdf:Description[@rdf:about=$metaid]/" "*[self::bqbiol:isEncodedBy or self::bqbiol:is]/" "rdf:Bag/rdf:li/@rdf:resource") extract_rdf_annotation = XPath(RDF_ANNOTATION_XPATH, namespaces=namespaces, smart_strings=False) else: RDF_ANNOTATION_XPATH = ns("sbml:annotation/rdf:RDF/" "rdf:Description[@rdf:about='%s']/" "bqbiol:isEncodedBy/" "rdf:Bag/rdf:li[@rdf:resource]") def extract_rdf_annotation(sbml_element, metaid): search_xpath = RDF_ANNOTATION_XPATH % metaid for i in sbml_element.iterfind(search_xpath): yield get_attrib(i, "rdf:resource") for i in sbml_element.iterfind(search_xpath .replace("isEncodedBy", "is")): yield get_attrib(i, "rdf:resource")
[docs]class CobraSBMLError(Exception): pass
[docs]def get_attrib(tag, attribute, type=lambda x: x, require=False): value = tag.get(ns(attribute)) if require and value is None: msg = "required attribute '%s' not found in tag '%s'" % \ (attribute, tag.tag) if tag.get("id") is not None: msg += " with id '%s'" % tag.get("id") elif tag.get("name") is not None: msg += " with name '%s'" % tag.get("name") raise CobraSBMLError(msg) return type(value) if value is not None else None
[docs]def set_attrib(xml, attribute_name, value): if value is None or value == "": return xml.set(ns(attribute_name), str(value))
[docs]def parse_stream(filename): """parses filename or compressed stream to xml""" try: if hasattr(filename, "read"): return parse(filename) elif filename.endswith(".gz"): with GzipFile(filename) as infile: return parse(infile) elif filename.endswith(".bz2"): with BZ2File(filename) as infile: return parse(infile) else: return parse(filename) except ParseError as e: raise CobraSBMLError("Malformed XML file: " + str(e))
# string utility functions
[docs]def clip(string, prefix): """clips a prefix from the beginning of a string if it exists >>> clip("R_pgi", "R_") "pgi" """ return string[len(prefix):] if string.startswith(prefix) else string
[docs]def strnum(number): """Utility function to convert a number to a string""" if isinstance(number, (Decimal, Basic, str)): return str(number) s = "%.15g" % number return s.rstrip(".")
[docs]def construct_gpr_xml(parent, expression): """create gpr xml under parent node""" if isinstance(expression, BoolOp): op = expression.op if isinstance(op, And): new_parent = SubElement(parent, AND_TAG) elif isinstance(op, Or): new_parent = SubElement(parent, OR_TAG) else: raise Exception("unsupported operation " + op.__class__) for arg in expression.values: construct_gpr_xml(new_parent, arg) elif isinstance(expression, Name): gene_elem = SubElement(parent, GENEREF_TAG) set_attrib(gene_elem, "fbc:geneProduct", "G_" + else: raise Exception("unsupported operation " + repr(expression))
[docs]def annotate_cobra_from_sbml(cobra_element, sbml_element): sbo_term = sbml_element.get("sboTerm") if sbo_term is not None: cobra_element.annotation["SBO"] = sbo_term meta_id = get_attrib(sbml_element, "metaid") if meta_id is None: return annotation = cobra_element.annotation for uri in extract_rdf_annotation(sbml_element, metaid="#" + meta_id): if not uri.startswith(""): warn("%s does not start with" % uri) continue try: provider, identifier = uri[23:].split("/", 1) except ValueError: warn("%s does not conform to" % uri) continue # handle multiple id's in the same database if provider in annotation: # make into a list if necessary if isinstance(annotation[provider], string_types): annotation[provider] = [annotation[provider]] annotation[provider].append(identifier) else: cobra_element.annotation[provider] = identifier
[docs]def annotate_sbml_from_cobra(sbml_element, cobra_element): if len(cobra_element.annotation) == 0: return # get the id so we can set the metaid tag = sbml_element.tag if tag.startswith(sbml_prefix) or tag[0] != "{": prefix = "" elif tag.startswith(fbc_prefix): prefix = fbc_prefix else: raise ValueError("Can not annotate " + repr(sbml_element)) id = sbml_element.get(prefix + "id") if len(id) == 0: raise ValueError("%s does not have id set" % repr(sbml_element)) set_attrib(sbml_element, "metaid", id) annotation = SubElement(sbml_element, ns("sbml:annotation")) rdf_desc = SubElement(SubElement(annotation, ns("rdf:RDF")), ns("rdf:Description")) set_attrib(rdf_desc, "rdf:about", "#" + id) bag = SubElement(SubElement(rdf_desc, ns("bqbiol:is")), ns("rdf:Bag")) for provider, identifiers in sorted(iteritems(cobra_element.annotation)): if provider == "SBO": set_attrib(sbml_element, "sboTerm", identifiers) continue if isinstance(identifiers, string_types): identifiers = (identifiers,) for identifier in identifiers: li = SubElement(bag, ns("rdf:li")) set_attrib(li, "rdf:resource", "" % (provider, identifier))
[docs]def parse_xml_into_model(xml, number=float): xml_model = xml.find(ns("sbml:model")) if get_attrib(xml_model, "fbc:strict") != "true": warn('loading SBML model without fbc:strict="true"') model_id = get_attrib(xml_model, "id") model = Model(model_id) = xml_model.get("name") model.compartments = {c.get("id"): c.get("name") for c in xml_model.findall(COMPARTMENT_XPATH)} # add metabolites for species in xml_model.findall(SPECIES_XPATH % 'false'): met = get_attrib(species, "id", require=True) met = Metabolite(clip(met, "M_")) = species.get("name") annotate_cobra_from_sbml(met, species) met.compartment = species.get("compartment") met.charge = get_attrib(species, "fbc:charge", int) met.formula = get_attrib(species, "fbc:chemicalFormula") model.add_metabolites([met]) # Detect boundary metabolites - In case they have been mistakenly # added. They should not actually appear in a model boundary_metabolites = {clip(i.get("id"), "M_") for i in xml_model.findall(SPECIES_XPATH % 'true')} # add genes for sbml_gene in xml_model.iterfind(GENES_XPATH): gene_id = get_attrib(sbml_gene, "fbc:id").replace(SBML_DOT, ".") gene = Gene(clip(gene_id, "G_")) = get_attrib(sbml_gene, "fbc:name") if is None: = get_attrib(sbml_gene, "fbc:label") annotate_cobra_from_sbml(gene, sbml_gene) model.genes.append(gene) def process_gpr(sub_xml): """recursively convert gpr xml to a gpr string""" if sub_xml.tag == OR_TAG: return "( " + ' or '.join(process_gpr(i) for i in sub_xml) + " )" elif sub_xml.tag == AND_TAG: return "( " + ' and '.join(process_gpr(i) for i in sub_xml) + " )" elif sub_xml.tag == GENEREF_TAG: gene_id = get_attrib(sub_xml, "fbc:geneProduct", require=True) return clip(gene_id, "G_") else: raise Exception("unsupported tag " + sub_xml.tag) bounds = {bound.get("id"): get_attrib(bound, "value", type=number) for bound in xml_model.iterfind(BOUND_XPATH)} # add reactions reactions = [] for sbml_reaction in xml_model.iterfind( ns("sbml:listOfReactions/sbml:reaction")): reaction = get_attrib(sbml_reaction, "id", require=True) reaction = Reaction(clip(reaction, "R_")) = sbml_reaction.get("name") annotate_cobra_from_sbml(reaction, sbml_reaction) lb_id = get_attrib(sbml_reaction, "fbc:lowerFluxBound", require=True) ub_id = get_attrib(sbml_reaction, "fbc:upperFluxBound", require=True) try: reaction.upper_bound = bounds[ub_id] reaction.lower_bound = bounds[lb_id] except KeyError as e: raise CobraSBMLError("No constant bound with id '%s'" % e.message) reactions.append(reaction) stoichiometry = defaultdict(lambda: 0) for species_reference in sbml_reaction.findall( ns("sbml:listOfReactants/sbml:speciesReference")): met_name = clip(species_reference.get("species"), "M_") stoichiometry[met_name] -= \ number(species_reference.get("stoichiometry")) for species_reference in sbml_reaction.findall( ns("sbml:listOfProducts/sbml:speciesReference")): met_name = clip(species_reference.get("species"), "M_") stoichiometry[met_name] += \ get_attrib(species_reference, "stoichiometry", type=number, require=True) # needs to have keys of metabolite objects, not ids object_stoichiometry = {} for met_id in stoichiometry: if met_id in boundary_metabolites: warn("Boundary metabolite '%s' used in reaction '%s'" % (met_id, continue try: metabolite = model.metabolites.get_by_id(met_id) except KeyError: warn("ignoring unknown metabolite '%s' in reaction %s" % (met_id, continue object_stoichiometry[metabolite] = stoichiometry[met_id] reaction.add_metabolites(object_stoichiometry) # set gene reaction rule gpr_xml = sbml_reaction.find(GPR_TAG) if gpr_xml is not None and len(gpr_xml) != 1: warn("ignoring invalid geneAssocation for " + repr(reaction)) gpr_xml = None gpr = process_gpr(gpr_xml[0]) if gpr_xml is not None else '' # remove outside parenthesis, if any if gpr.startswith("(") and gpr.endswith(")"): gpr = gpr[1:-1].strip() gpr = gpr.replace(SBML_DOT, ".") reaction.gene_reaction_rule = gpr model.add_reactions(reactions) # objective coefficients are handled after all reactions are added obj_list = xml_model.find(ns("fbc:listOfObjectives")) if obj_list is None: warn("listOfObjectives element not found") return model target_objective = get_attrib(obj_list, "fbc:activeObjective") obj_query = OBJECTIVES_XPATH % target_objective for sbml_objective in obj_list.findall(obj_query): rxn_id = clip(get_attrib(sbml_objective, "fbc:reaction"), "R_") try: objective_reaction = model.reactions.get_by_id(rxn_id) except KeyError as e: raise CobraSBMLError("Objective reaction '%s' not found" % rxn_id) objective_reaction.objective_coefficient = \ get_attrib(sbml_objective, "fbc:coefficient", type=number) return model
[docs]def model_to_xml(cobra_model, units=True): xml = Element("sbml", xmlns=namespaces["sbml"], level="3", version="1", sboTerm="SBO:0000624") set_attrib(xml, "fbc:required", "false") xml_model = SubElement(xml, "model") set_attrib(xml_model, "fbc:strict", "true") if is not None: xml_model.set("id", if is not None: xml_model.set("name", # if using units, add in mmol/gdw/hr if units: unit_def = SubElement( SubElement(xml_model, "listOfUnitDefinitions"), "unitDefinition", id="mmol_per_gDW_per_hr") list_of_units = SubElement(unit_def, "listOfUnits") SubElement(list_of_units, "unit", kind="mole", scale="-3", multiplier="1", exponent="1") SubElement(list_of_units, "unit", kind="gram", scale="0", multiplier="1", exponent="-1") SubElement(list_of_units, "unit", kind="second", scale="0", multiplier="3600", exponent="-1") # create the element for the flux objective obj_list_tmp = SubElement(xml_model, ns("fbc:listOfObjectives")) set_attrib(obj_list_tmp, "fbc:activeObjective", "obj") obj_list_tmp = SubElement(obj_list_tmp, ns("fbc:objective")) set_attrib(obj_list_tmp, "fbc:id", "obj") set_attrib(obj_list_tmp, "fbc:type", "maximize") flux_objectives_list = SubElement(obj_list_tmp, ns("fbc:listOfFluxObjectives")) # create the element for the flux bound parameters parameter_list = SubElement(xml_model, "listOfParameters") param_attr = {"constant": "true"} if units: param_attr["units"] = "mmol_per_gDW_per_hr" # the most common bounds are the minimum, maxmium, and 0 if len(cobra_model.reactions) > 0: min_value = min(cobra_model.reactions.list_attr("lower_bound")) max_value = max(cobra_model.reactions.list_attr("upper_bound")) else: min_value = -1000 max_value = 1000 SubElement(parameter_list, "parameter", value=strnum(min_value), id="cobra_default_lb", sboTerm="SBO:0000626", **param_attr) SubElement(parameter_list, "parameter", value=strnum(max_value), id="cobra_default_ub", sboTerm="SBO:0000626", **param_attr) SubElement(parameter_list, "parameter", value="0", id="cobra_0_bound", sboTerm="SBO:0000626", **param_attr) def create_bound(reaction, bound_type): """returns the str id of the appropriate bound for the reaction The bound will also be created if necessary""" value = getattr(reaction, bound_type) if value == min_value: return "cobra_default_lb" elif value == 0: return "cobra_0_bound" elif value == max_value: return "cobra_default_ub" else: param_id = "R_" + + "_" + bound_type SubElement(parameter_list, "parameter", id=param_id, value=strnum(value), sboTerm="SBO:0000625", **param_attr) return param_id # add in compartments compartmenst_list = SubElement(xml_model, "listOfCompartments") compartments = cobra_model.compartments for compartment, name in iteritems(compartments): SubElement(compartmenst_list, "compartment", id=compartment, name=name, constant="true") # add in metabolites species_list = SubElement(xml_model, "listOfSpecies") for met in cobra_model.metabolites: species = SubElement(species_list, "species", id="M_" +, # Useless required SBML parameters constant="false", boundaryCondition="false", hasOnlySubstanceUnits="false") set_attrib(species, "name", annotate_sbml_from_cobra(species, met) set_attrib(species, "compartment", met.compartment) set_attrib(species, "fbc:charge", met.charge) set_attrib(species, "fbc:chemicalFormula", met.formula) # add in genes if len(cobra_model.genes) > 0: genes_list = SubElement(xml_model, GENELIST_TAG) for gene in cobra_model.genes: gene_id =".", SBML_DOT) sbml_gene = SubElement(genes_list, GENE_TAG) set_attrib(sbml_gene, "fbc:id", "G_" + gene_id) name = if name is None or len(name) == 0: name = set_attrib(sbml_gene, "fbc:label", gene_id) set_attrib(sbml_gene, "fbc:name", annotate_sbml_from_cobra(sbml_gene, gene) # add in reactions reactions_list = SubElement(xml_model, "listOfReactions") for reaction in cobra_model.reactions: id = "R_" + sbml_reaction = SubElement( reactions_list, "reaction", id=id, # Useless required SBML parameters fast="false", reversible=str(reaction.lower_bound < 0).lower()) set_attrib(sbml_reaction, "name", annotate_sbml_from_cobra(sbml_reaction, reaction) # add in bounds set_attrib(sbml_reaction, "fbc:upperFluxBound", create_bound(reaction, "upper_bound")) set_attrib(sbml_reaction, "fbc:lowerFluxBound", create_bound(reaction, "lower_bound")) # objective coefficient if reaction.objective_coefficient != 0: objective = SubElement(flux_objectives_list, ns("fbc:fluxObjective")) set_attrib(objective, "fbc:reaction", id) set_attrib(objective, "fbc:coefficient", strnum(reaction.objective_coefficient)) # stoichiometry reactants = {} products = {} for metabolite, stoichiomety in iteritems(reaction._metabolites): met_id = "M_" + if stoichiomety > 0: products[met_id] = strnum(stoichiomety) else: reactants[met_id] = strnum(-stoichiomety) if len(reactants) > 0: reactant_list = SubElement(sbml_reaction, "listOfReactants") for met_id, stoichiomety in sorted(iteritems(reactants)): SubElement(reactant_list, "speciesReference", species=met_id, stoichiometry=stoichiomety, constant="true") if len(products) > 0: product_list = SubElement(sbml_reaction, "listOfProducts") for met_id, stoichiomety in sorted(iteritems(products)): SubElement(product_list, "speciesReference", species=met_id, stoichiometry=stoichiomety, constant="true") # gene reaction rule gpr = reaction.gene_reaction_rule if gpr is not None and len(gpr) > 0: gpr = gpr.replace(".", SBML_DOT) gpr_xml = SubElement(sbml_reaction, GPR_TAG) try: parsed = parse_gpr(gpr)[0] construct_gpr_xml(gpr_xml, parsed.body) except Exception as e: print("failed on '%s' in %s" % (reaction.gene_reaction_rule, repr(reaction))) raise e return xml
[docs]def read_sbml_model(filename, number=float, **kwargs): xmlfile = parse_stream(filename) xml = xmlfile.getroot() # use libsbml if not l3v1 with fbc v2 if xml.get("level") != "3" or xml.get("version") != "1" or \ get_attrib(xml, "fbc:required") is None: if libsbml is None: raise Exception("libSBML required for fbc < 2") # libsbml needs a file string, so write to temp file if a file handle if hasattr(filename, "read"): with NamedTemporaryFile(suffix=".xml", delete=False) as outfile: xmlfile.write(outfile, encoding="UTF-8") filename = return read_sbml2(filename, **kwargs) try: return parse_xml_into_model(xml, number=number, **kwargs) except Exception: raise CobraSBMLError( "Something went wrong reading the model. You can get a detailed " "report using the `` function " "or using the online validator at")
id_required = {ns(i) for i in ("sbml:model", "sbml:reaction:", "sbml:species", "fbc:geneProduct", "sbml:compartment", "sbml:paramter", "sbml:UnitDefinition", "fbc:objective")} invalid_id_detector = re.compile("|".join(re.escape(i[0]) for i in _renames))
[docs]def validate_sbml_model(filename, check_model=True): """Returns the model along with a list of errors. Parameters ---------- filename : str The filename of the SBML model to be validated. check_model: bool, optional Whether to also check some basic model properties such as reaction boundaries and compartment formulas. Returns ------- model : :class:`~cobra.core.Model.Model` object The cobra model if the file could be read succesfully or None otherwise. errors : dict Warnings and errors grouped by their respective types. Raises ------ CobraSBMLError If the file is not a valid SBML Level 3 file with FBC. """ xmlfile = parse_stream(filename) xml = xmlfile.getroot() # use libsbml if not l3v1 with fbc v2 if xml.get("level") != "3" or xml.get("version") != "1" or \ get_attrib(xml, "fbc:required") is None: raise CobraSBMLError("XML is not SBML level 3 v1 with fbc v2") errors = {k: [] for k in ("validator", "warnings", "SBML errors", "other")} def err(err_msg, group="validator"): errors[group].append(err_msg) # make sure there is exactly one model xml_models = xml.findall(ns("sbml:model")) if len(xml_models) > 1: err("More than 1 SBML model detected in file") elif len(xml_models) == 0: err("No SBML model detected in file") else: xml_model = xml_models[0] # make sure all sbml id's are valid all_ids = set() for element in xmlfile.iter(): if element.tag.startswith(fbc_prefix): prefix = fbc_prefix elif element.tag.startswith(sbml_prefix): prefix = "" else: continue str_id = element.get(prefix + "id", None) element_name = element.tag.split("}")[-1] id_repr = "%s id '%s' " % (element_name, str_id) if str_id is None or len(str_id) == 0: if element.tag in id_required: err(element_name + " missing id") else: if str_id in all_ids: err("duplicate id for " + id_repr) all_ids.add(str_id) try: str_id.encode("ascii") except UnicodeEncodeError as e: err("invalid character '%s' found in %s" % (str_id[e.start:e.end], id_repr)) if bad_chars = "".join(invalid_id_detector.findall(str_id)) err("invalid character%s '%s' found in %s" % ("s" if len(bad_chars) > 1 else "", bad_chars, id_repr)) if not str_id[0].isalpha(): err("%s does not start with alphabet character" % id_repr) # check SBO terms for element in xml.findall(".//*[@sboTerm]"): sbo_term = element.get("sboTerm") if not sbo_term.startswith("SBO:"): err("sboTerm '%s' does not begin with 'SBO:'" % sbo_term) # ensure can be made into model # all warnings generated while loading will be logged as errors with catch_warnings(record=True) as warning_list: simplefilter("always") try: model = parse_xml_into_model(xml) except CobraSBMLError as e: err(str(e), "SBML errors") return (None, errors) except Exception as e: err(str(e), "other") return (None, errors) errors["warnings"].extend(str(i.message) for i in warning_list) # check genes xml_genes = { get_attrib(i, "fbc:id").replace(SBML_DOT, ".") for i in xml_model.iterfind(GENES_XPATH)} for gene in model.genes: if "G_" + not in xml_genes and not in xml_genes: err("No gene specfied with id 'G_%s'" % if check_model: errors["validator"].extend(check_reaction_bounds(model)) errors["validator"].extend(check_metabolite_compartment_formula(model)) return model, errors
[docs]def write_sbml_model(cobra_model, filename, use_fbc_package=True, **kwargs): if not use_fbc_package: if libsbml is None: raise Exception("libSBML required to write non-fbc models") write_sbml2(cobra_model, filename, use_fbc_package=False, **kwargs) return # create xml xml = model_to_xml(cobra_model, **kwargs) write_args = {"encoding": "UTF-8", "xml_declaration": True} if _with_lxml: write_args["pretty_print"] = True write_args["pretty_print"] = True else: indent_xml(xml) # write xml to file should_close = True if hasattr(filename, "write"): xmlfile = filename should_close = False elif filename.endswith(".gz"): xmlfile = GzipFile(filename, "wb") elif filename.endswith(".bz2"): xmlfile = BZ2File(filename, "wb") else: xmlfile = open(filename, "wb") ElementTree(xml).write(xmlfile, **write_args) if should_close: xmlfile.close()
# inspired by
[docs]def indent_xml(elem, level=0): """indent xml for pretty printing""" i = "\n" + level * " " if len(elem): if not elem.text or not elem.text.strip(): elem.text = i + " " if not elem.tail or not elem.tail.strip(): elem.tail = i for elem in elem: indent_xml(elem, level + 1) if not elem.tail or not elem.tail.strip(): elem.tail = i else: if level and (not elem.tail or not elem.tail.strip()): elem.tail = i