def addMetabolomicsReaction(model, metabolites, react_name, coefficient_str=1):
print(react_name, ":", metabolites)
# Build a reaction
coefficient_str = str(coefficient_str)
reaction_str = coefficient_str + (" + " + coefficient_str).join(
metabolites) + " <==> " + react_name + "_c"
reaction = Reaction(react_name)
reaction.name = react_name
reaction.subsystem = 'Metabolomics integration'
# Add the reaction to the model
model.add_reactions([reaction])
reaction.build_reaction_from_string(reaction_str)
#print(reaction,":::::",reaction_str)
return reaction
def convert_to_irreversible(model):
"""Split reversible reactions into two irreversible reactions
These two reactions will proceed in opposite directions. This
guarentees that all reactions in the model will only allow
positive flux values, which is useful for some modeling problems.
Arguments
----------
* model: cobra.Model ~ A Model object which will be modified in place.
"""
#warn("deprecated, not applicable for optlang solvers", DeprecationWarning)
reactions_to_add = []
coefficients = {}
for reaction in model.reactions:
# If a reaction is reverse only, the forward reaction (which
# will be constrained to 0) will be left in the model.
if reaction.lower_bound < 0 and reaction.upper_bound > 0:
reverse_reaction = Reaction(reaction.id + "_reverse")
reverse_reaction.lower_bound = max(0, -reaction.upper_bound)
reverse_reaction.upper_bound = -reaction.lower_bound
coefficients[
reverse_reaction] = reaction.objective_coefficient * -1
reaction.lower_bound = max(0, reaction.lower_bound)
reaction.upper_bound = max(0, reaction.upper_bound)
# Make the directions aware of each other
reaction.notes["reflection"] = reverse_reaction.id
reverse_reaction.notes["reflection"] = reaction.id
reaction_dict = {
k: v * -1
for k, v in reaction._metabolites.items()
}
reverse_reaction.add_metabolites(reaction_dict)
reverse_reaction._model = reaction._model
reverse_reaction._genes = reaction._genes
for gene in reaction._genes:
gene._reaction.add(reverse_reaction)
reverse_reaction.subsystem = reaction.subsystem
reverse_reaction._gene_reaction_rule = reaction._gene_reaction_rule
reactions_to_add.append(reverse_reaction)
model.add_reactions(reactions_to_add)
set_objective(model, coefficients, additive=True)
def convert_to_irreversible(cobra_model):
"""Split reversible reactions into two irreversible reactions
These two reactions will proceed in opposite directions. This
guarentees that all reactions in the model will only allow
positive flux values, which is useful for some modeling problems.
cobra_model: A Model object which will be modified in place.
"""
warn("deprecated, not applicable for optlang solvers", DeprecationWarning)
reactions_to_add = []
coefficients = {}
for reaction in cobra_model.reactions:
# If a reaction is reverse only, the forward reaction (which
# will be constrained to 0) will be left in the model.
if reaction.lower_bound < 0:
reverse_reaction = Reaction(reaction.id + "_reverse")
reverse_reaction.lower_bound = max(0, -reaction.upper_bound)
reverse_reaction.upper_bound = -reaction.lower_bound
coefficients[
reverse_reaction] = reaction.objective_coefficient * -1
reaction.lower_bound = max(0, reaction.lower_bound)
reaction.upper_bound = max(0, reaction.upper_bound)
# Make the directions aware of each other
reaction.notes["reflection"] = reverse_reaction.id
reverse_reaction.notes["reflection"] = reaction.id
reaction_dict = {k: v * -1
for k, v in iteritems(reaction._metabolites)}
reverse_reaction.add_metabolites(reaction_dict)
reverse_reaction._model = reaction._model
reverse_reaction._genes = reaction._genes
for gene in reaction._genes:
gene._reaction.add(reverse_reaction)
reverse_reaction.subsystem = reaction.subsystem
reverse_reaction._gene_reaction_rule = reaction._gene_reaction_rule
reactions_to_add.append(reverse_reaction)
cobra_model.add_reactions(reactions_to_add)
set_objective(cobra_model, coefficients, additive=True)
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.
Parameters
----------
sbml_filename: string
old_sbml: bool
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: bool
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: bool
deprecated
use_hyphens: bool
If True, double underscores (__) in an SBML ID will be converted to
hyphens
Returns
-------
Model : The parsed cobra model
"""
if not libsbml:
raise ImportError('create_cobra_model_from_sbml_file '
'requires python-libsbml')
__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", DeprecationWarning)
model_doc = libsbml.readSBML(sbml_filename)
if model_doc.getPlugin("fbc") is not 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 iteritems(compartment_dict)])
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")
# set charge to the one from notes if not assigend before
# the same
tmp_metabolite.charge = note_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 = []
coefficients = {}
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
objective_coefficient = parameter_dict.get(
'objective_coefficient', parameter_dict.get(
'objective_coefficient', __default_objective_coefficient))
if objective_coefficient != 0:
coefficients[reaction] = 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)
set_objective(cobra_model, coefficients)
return cobra_model
def from_mat_struct(mat_struct, model_id=None, inf=inf):
"""create a model from the COBRA toolbox struct
The struct will be a dict read in by scipy.io.loadmat
"""
m = mat_struct
if m.dtype.names is None:
raise ValueError("not a valid mat struct")
if not {"rxns", "mets", "S", "lb", "ub"} <= set(m.dtype.names):
raise ValueError("not a valid mat struct")
if "c" in m.dtype.names:
c_vec = m["c"][0, 0]
else:
c_vec = None
warn("objective vector 'c' not found")
model = Model()
if model_id is not None:
model.id = model_id
elif "description" in m.dtype.names:
description = m["description"][0, 0][0]
if not isinstance(description, string_types) and len(description) > 1:
model.id = description[0]
warn("Several IDs detected, only using the first.")
else:
model.id = description
else:
model.id = "imported_model"
for i, name in enumerate(m["mets"][0, 0]):
new_metabolite = Metabolite()
new_metabolite.id = str(name[0][0])
if all(var in m.dtype.names
for var in ['metComps', 'comps', 'compNames']):
comp_index = m["metComps"][0, 0][i][0] - 1
new_metabolite.compartment = m['comps'][0, 0][comp_index][0][0]
if new_metabolite.compartment not in model.compartments:
comp_name = m['compNames'][0, 0][comp_index][0][0]
model.compartments[new_metabolite.compartment] = comp_name
else:
new_metabolite.compartment = _get_id_compartment(new_metabolite.id)
if new_metabolite.compartment not in model.compartments:
model.compartments[
new_metabolite.compartment] = new_metabolite.compartment
try:
new_metabolite.name = str(m["metNames"][0, 0][i][0][0])
except (IndexError, ValueError):
pass
try:
new_metabolite.formula = str(m["metFormulas"][0][0][i][0][0])
except (IndexError, ValueError):
pass
try:
new_metabolite.charge = float(m["metCharge"][0, 0][i][0])
int_charge = int(new_metabolite.charge)
if new_metabolite.charge == int_charge:
new_metabolite.charge = int_charge
except (IndexError, ValueError):
pass
model.add_metabolites([new_metabolite])
new_reactions = []
coefficients = {}
for i, name in enumerate(m["rxns"][0, 0]):
new_reaction = Reaction()
new_reaction.id = str(name[0][0])
new_reaction.lower_bound = float(m["lb"][0, 0][i][0])
new_reaction.upper_bound = float(m["ub"][0, 0][i][0])
if isinf(new_reaction.lower_bound) and new_reaction.lower_bound < 0:
new_reaction.lower_bound = -inf
if isinf(new_reaction.upper_bound) and new_reaction.upper_bound > 0:
new_reaction.upper_bound = inf
if c_vec is not None:
coefficients[new_reaction] = float(c_vec[i][0])
try:
new_reaction.gene_reaction_rule = str(m['grRules'][0, 0][i][0][0])
except (IndexError, ValueError):
pass
try:
new_reaction.name = str(m["rxnNames"][0, 0][i][0][0])
except (IndexError, ValueError):
pass
try:
new_reaction.subsystem = str(m['subSystems'][0, 0][i][0][0])
except (IndexError, ValueError):
pass
new_reactions.append(new_reaction)
model.add_reactions(new_reactions)
set_objective(model, coefficients)
coo = scipy_sparse.coo_matrix(m["S"][0, 0])
for i, j, v in zip(coo.row, coo.col, coo.data):
model.reactions[j].add_metabolites({model.metabolites[i]: v})
return model
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.
Parameters
----------
sbml_filename: string
old_sbml: bool
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: bool
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: bool
deprecated
use_hyphens: bool
If True, double underscores (__) in an SBML ID will be converted to
hyphens
Returns
-------
Model : The parsed cobra model
"""
if not libsbml:
raise ImportError('create_cobra_model_from_sbml_file '
'requires python-libsbml')
__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", DeprecationWarning)
model_doc = libsbml.readSBML(sbml_filename)
if model_doc.getPlugin("fbc") is not 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 iteritems(compartment_dict)])
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")
# set charge to the one from notes if not assigend before
# the same
tmp_metabolite.charge = note_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 = []
coefficients = {}
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
objective_coefficient = parameter_dict.get(
'objective_coefficient', parameter_dict.get(
'objective_coefficient', __default_objective_coefficient))
if objective_coefficient != 0:
coefficients[reaction] = 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)
set_objective(cobra_model, coefficients)
return cobra_model
def from_mat_struct(mat_struct, model_id=None, inf=inf):
"""create a model from the COBRA toolbox struct
The struct will be a dict read in by scipy.io.loadmat
"""
m = mat_struct
if m.dtype.names is None:
raise ValueError("not a valid mat struct")
if not {"rxns", "mets", "S", "lb", "ub"} <= set(m.dtype.names):
raise ValueError("not a valid mat struct")
if "c" in m.dtype.names:
c_vec = m["c"][0, 0]
else:
c_vec = None
warn("objective vector 'c' not found")
model = Model()
if model_id is not None:
model.id = model_id
elif "description" in m.dtype.names:
description = m["description"][0, 0][0]
if not isinstance(description, string_types) and len(description) > 1:
model.id = description[0]
warn("Several IDs detected, only using the first.")
else:
model.id = description
else:
model.id = "imported_model"
for i, name in enumerate(m["mets"][0, 0]):
new_metabolite = Metabolite()
new_metabolite.id = str(name[0][0])
if all(var in m.dtype.names for var in
['metComps', 'comps', 'compNames']):
comp_index = m["metComps"][0, 0][i][0] - 1
new_metabolite.compartment = m['comps'][0, 0][comp_index][0][0]
if new_metabolite.compartment not in model.compartments:
comp_name = m['compNames'][0, 0][comp_index][0][0]
model.compartments[new_metabolite.compartment] = comp_name
else:
new_metabolite.compartment = _get_id_compartment(new_metabolite.id)
if new_metabolite.compartment not in model.compartments:
model.compartments[
new_metabolite.compartment] = new_metabolite.compartment
try:
new_metabolite.name = str(m["metNames"][0, 0][i][0][0])
except (IndexError, ValueError):
pass
try:
new_metabolite.formula = str(m["metFormulas"][0][0][i][0][0])
except (IndexError, ValueError):
pass
try:
new_metabolite.charge = float(m["metCharge"][0, 0][i][0])
int_charge = int(new_metabolite.charge)
if new_metabolite.charge == int_charge:
new_metabolite.charge = int_charge
except (IndexError, ValueError):
pass
model.add_metabolites([new_metabolite])
new_reactions = []
coefficients = {}
for i, name in enumerate(m["rxns"][0, 0]):
new_reaction = Reaction()
new_reaction.id = str(name[0][0])
new_reaction.lower_bound = float(m["lb"][0, 0][i][0])
new_reaction.upper_bound = float(m["ub"][0, 0][i][0])
if isinf(new_reaction.lower_bound) and new_reaction.lower_bound < 0:
new_reaction.lower_bound = -inf
if isinf(new_reaction.upper_bound) and new_reaction.upper_bound > 0:
new_reaction.upper_bound = inf
if c_vec is not None:
coefficients[new_reaction] = float(c_vec[i][0])
try:
new_reaction.gene_reaction_rule = str(m['grRules'][0, 0][i][0][0])
except (IndexError, ValueError):
pass
try:
new_reaction.name = str(m["rxnNames"][0, 0][i][0][0])
except (IndexError, ValueError):
pass
try:
new_reaction.subsystem = str(m['subSystems'][0, 0][i][0][0])
except (IndexError, ValueError):
pass
new_reactions.append(new_reaction)
model.add_reactions(new_reactions)
set_objective(model, coefficients)
coo = scipy_sparse.coo_matrix(m["S"][0, 0])
for i, j, v in zip(coo.row, coo.col, coo.data):
model.reactions[j].add_metabolites({model.metabolites[i]: v})
return model