def ubiquitize_model(in_sbml,
chebi,
groups_sbml,
ub_s_ids=None,
ub_chebi_ids=None):
"""
Infers and marks ubiquitous species in the model.
:param in_sbml: str, path to the input SBML file
:param chebi: mod_sbml.onto.obo_ontology.Ontology ChEBI ontology
:param groups_sbml: str, path to the output SBML file (with groups extension)
:param ub_s_ids: optional, ids of ubiquitous species (will be inferred if set to None)
:param ub_chebi_ids: optional, ids of ubiquitous ChEBI terms (will be inferred if set to None)
:return: tuple (s_id2chebi_id, ub_s_ids): dict {species_id: ChEBI_term_id}, collection of ubiquitous species_ids.
"""
input_doc = libsbml.SBMLReader().readSBML(in_sbml)
input_model = input_doc.getModel()
annotate_metabolites(input_model, chebi)
logging.info("mapping species to ChEBI")
s_id2chebi_id = get_species_id2chebi_id(input_model)
_, ub_s_ids = get_ub_elements(input_model, chebi, s_id2chebi_id,
ub_chebi_ids, ub_s_ids)
save_as_comp_generalized_sbml(input_model, None, groups_sbml, {}, {},
ub_s_ids, chebi)
return s_id2chebi_id, ub_s_ids
def ubiquitize_model(in_sbml, chebi, groups_sbml, ub_s_ids=None, ub_chebi_ids=None):
"""
Infers and marks ubiquitous species in the model.
:param in_sbml: str, path to the input SBML file
:param chebi: mod_sbml.onto.obo_ontology.Ontology ChEBI ontology
:param groups_sbml: str, path to the output SBML file (with groups extension)
:param ub_s_ids: optional, ids of ubiquitous species (will be inferred if set to None)
:param ub_chebi_ids: optional, ids of ubiquitous ChEBI terms (will be inferred if set to None)
:return: tuple (s_id2chebi_id, ub_s_ids): dict {species_id: ChEBI_term_id}, collection of ubiquitous species_ids.
"""
input_doc = libsbml.SBMLReader().readSBML(in_sbml)
input_model = input_doc.getModel()
annotate_metabolites(input_model, chebi)
logging.info("mapping species to ChEBI")
s_id2chebi_id = get_species_id2chebi_id(input_model)
_, ub_s_ids = get_ub_elements(input_model, chebi, s_id2chebi_id, ub_chebi_ids, ub_s_ids)
save_as_comp_generalized_sbml(input_model, None, groups_sbml, {}, {}, ub_s_ids, chebi)
return s_id2chebi_id, ub_s_ids
def generalize_model(in_sbml, chebi, groups_sbml, out_sbml, ub_s_ids=None, ub_chebi_ids=None, ignore_biomass=True):
"""
Generalizes a model.
:param in_sbml: str, path to the input SBML file
:param chebi: mod_sbml.onto.obo_ontology.Ontology ChEBI ontology
:param groups_sbml: str, path to the output SBML file (with groups extension)
:param out_sbml: str, path to the output SBML file (generalized)
:param ub_s_ids: optional, ids of ubiquitous species (will be inferred if set to None)
:param ub_chebi_ids: optional, ids of ubiquitous ChEBI terms (will be inferred if set to None)
:param ignore_biomass: boolean, whether to ignore the biomass reaction (and its stoichiometry preserving constraint)
:return: tuple (r_id2g_eq, s_id2gr_id, s_id2chebi_id, ub_s_ids):
dict {reaction_id: reaction_group_id}, dict {species_id: species_group_id}, dict {species_id: ChEBI_term_id},
collection of ubiquitous species_ids.
"""
# input_model
input_doc = libsbml.SBMLReader().readSBML(in_sbml)
input_model = input_doc.getModel()
r_ids_to_ignore = get_biomass_r_ids(input_model) if ignore_biomass else None
remove_is_a_reactions(input_model)
annotate_metabolites(input_model, chebi)
# TODO: fix comp separation
# separate_boundary_metabolites(input_model)
remove_unused_elements(input_model)
logging.info("mapping species to ChEBI")
s_id2chebi_id = get_species_id2chebi_id(input_model)
ub_chebi_ids, ub_s_ids = get_ub_elements(input_model, chebi, s_id2chebi_id, ub_chebi_ids, ub_s_ids)
terms = (t for t in (chebi.get_term(t_id) for t_id in s_id2chebi_id.values()) if t)
old_onto_len = len(chebi)
filter_ontology(chebi, terms, relationships=EQUIVALENT_RELATIONSHIPS, min_deepness=3)
logging.info('Filtered the ontology from %d terms to %d' % (old_onto_len, len(chebi)))
threshold = min(max(3, int(0.1 * input_model.getNumReactions())), UBIQUITOUS_THRESHOLD)
s_id2clu, ub_s_ids = generalize_species(input_model, s_id2chebi_id, ub_s_ids, chebi, ub_chebi_ids, threshold,
r_ids_to_ignore=r_ids_to_ignore)
logging.info("generalized species")
r_id2clu = generalize_reactions(input_model, s_id2clu, s_id2chebi_id, ub_chebi_ids,
r_ids_to_ignore=r_ids_to_ignore)
logging.info("generalized reactions")
clu2s_ids = {(c_id, term): s_ids for ((c_id, (term, )), s_ids) in invert_map(s_id2clu).items()}
r_id2g_eq, s_id2gr_id = save_as_comp_generalized_sbml(input_model, out_sbml, groups_sbml, r_id2clu, clu2s_ids,
ub_s_ids, chebi)
return r_id2g_eq, s_id2gr_id, s_id2chebi_id, ub_s_ids
def generalize_model(in_sbml,
chebi,
groups_sbml,
out_sbml,
ub_s_ids=None,
ub_chebi_ids=None,
ignore_biomass=True):
"""
Generalizes a model.
:param in_sbml: str, path to the input SBML file
:param chebi: mod_sbml.onto.obo_ontology.Ontology ChEBI ontology
:param groups_sbml: str, path to the output SBML file (with groups extension)
:param out_sbml: str, path to the output SBML file (generalized)
:param ub_s_ids: optional, ids of ubiquitous species (will be inferred if set to None)
:param ub_chebi_ids: optional, ids of ubiquitous ChEBI terms (will be inferred if set to None)
:param ignore_biomass: boolean, whether to ignore the biomass reaction (and its stoichiometry preserving constraint)
:return: tuple (r_id2g_eq, s_id2gr_id, s_id2chebi_id, ub_s_ids):
dict {reaction_id: reaction_group_id}, dict {species_id: species_group_id}, dict {species_id: ChEBI_term_id},
collection of ubiquitous species_ids.
"""
# input_model
input_doc = libsbml.SBMLReader().readSBML(in_sbml)
input_model = input_doc.getModel()
r_ids_to_ignore = get_biomass_r_ids(
input_model) if ignore_biomass else None
remove_is_a_reactions(input_model)
annotate_metabolites(input_model, chebi)
# TODO: fix comp separation
# separate_boundary_metabolites(input_model)
remove_unused_elements(input_model)
logging.info("mapping species to ChEBI")
s_id2chebi_id = get_species_id2chebi_id(input_model)
ub_chebi_ids, ub_s_ids = get_ub_elements(input_model, chebi, s_id2chebi_id,
ub_chebi_ids, ub_s_ids)
terms = (t for t in (chebi.get_term(t_id)
for t_id in s_id2chebi_id.values()) if t)
old_onto_len = len(chebi)
filter_ontology(chebi,
terms,
relationships=EQUIVALENT_RELATIONSHIPS,
min_deepness=3)
logging.info('Filtered the ontology from %d terms to %d' %
(old_onto_len, len(chebi)))
threshold = min(max(3, int(0.1 * input_model.getNumReactions())),
UBIQUITOUS_THRESHOLD)
s_id2clu, ub_s_ids = generalize_species(input_model,
s_id2chebi_id,
ub_s_ids,
chebi,
ub_chebi_ids,
threshold,
r_ids_to_ignore=r_ids_to_ignore)
logging.info("generalized species")
r_id2clu = generalize_reactions(input_model,
s_id2clu,
s_id2chebi_id,
ub_chebi_ids,
r_ids_to_ignore=r_ids_to_ignore)
logging.info("generalized reactions")
clu2s_ids = {(c_id, term): s_ids
for ((c_id, (term, )), s_ids) in invert_map(s_id2clu).items()}
r_id2g_eq, s_id2gr_id = save_as_comp_generalized_sbml(
input_model, out_sbml, groups_sbml, r_id2clu, clu2s_ids, ub_s_ids,
chebi)
return r_id2g_eq, s_id2gr_id, s_id2chebi_id, ub_s_ids
