def write_sbml(doc,
filepath,
validate=True,
program_name=None,
program_version=None,
show_errors=True):
"""
Write SBMLDocument to file.
:param doc: SBMLDocument to write
:param filepath: output file to write
:param validate: flag for validation (True: full validation, False: no validation)
:param program_name: Program name for SBML file
:param program_version: Program version for SBML file
:return:
"""
writer = libsbml.SBMLWriter()
if program_name:
writer.setProgramName(program_name)
if program_version:
writer.setProgramVersion(program_version)
writer.writeSBMLToFile(doc, filepath)
# validate the model with units (only for small models)
# This validates the written file
if validate:
if validate is True:
validation.check_sbml(filepath)
elif validate is validation.VALIDATION_NO_UNITS:
validation.check_sbml(filepath,
units_consistency=False,
log_errors=True)
def test_SBMLWriter_L3_create(self):
w = libsbml.SBMLWriter()
self.assert_(w != None)
_dummyList = [w]
_dummyList[:] = []
del _dummyList
pass
def save_cbmodel(model, filename, flavor=Flavor.FBC2.value):
""" Save a constraint-based model to an SBML file.
Arguments:
model (Model): model
filename (str): file path
flavor (str): (optional, currently available: 'cobra', 'fbc2', 'bigg')
"""
document = sb.SBMLDocument(DEFAULT_SBML_LEVEL, DEFAULT_SBML_VERSION)
sbml_model = document.createModel(model.id)
if flavor in {Flavor.BIGG.value, Flavor.FBC2.value}:
document.enablePackage(sb.FbcExtension.getXmlnsL3V1V2(), 'fbc', True)
fbc_model = sbml_model.getPlugin('fbc')
fbc_model.setStrict(True)
document.setPackageRequired('fbc', False)
save_compartments(model, sbml_model)
save_metabolites(model, sbml_model, flavor)
save_reactions(model, sbml_model)
save_cb_parameters(model, sbml_model, flavor)
save_gpr_associations(model, sbml_model, flavor)
save_metadata(model, sbml_model)
writer = sb.SBMLWriter()
writer.writeSBML(document, filename)
def write_sbml(sbml, filename):
"""
Write an SBML object to the specified path.
"""
change_modified_date(sbml)
writer = libsbml.SBMLWriter()
writer.writeSBMLToFile(sbml, filename)
def main(args):
"""usage: echoSBML.py input-filename output-filename
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
infile = args[1]
outfile = args[2]
if not os.path.exists(infile):
print("[Error] %s : No such file." % infile)
sys.exit(1)
reader = libsbml.SBMLReader()
writer = libsbml.SBMLWriter()
sbmldoc = reader.readSBML(infile)
if sbmldoc.getNumErrors() > 0:
if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
sbmldoc.printErrors()
elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
sbmldoc.printErrors()
else:
# Handle other error cases here.
sbmldoc.printErrors()
sys.exit(1)
writer.writeSBML(sbmldoc, outfile)
print("[OK] Echoed %s to %s" % (infile, outfile))
def main():
sbml_file_template = 'ERBB_RAS_AKT_Drugs_r389936_withObs_withSigma.sbml'
sbml_file_new = 'CS_Signalling_ERBB_RAS_AKT_CCLE_petab.xml'
sbml_reader = libsbml.SBMLReader()
sbml_document = sbml_reader.readSBML(sbml_file_template)
sbml_model = sbml_document.getModel()
petab.log_sbml_errors(sbml_document)
# fix units
set_species_unit_to_nanomole(sbml_model)
# Add observable and sigma
add_observables(sbml_model)
petab.globalize_parameters(sbml_model)
gene_specific_scaling_non_const(sbml_model)
# Write updated model
sbml_writer = libsbml.SBMLWriter()
sbml_writer.writeSBMLToFile(sbml_document, sbml_file_new)
# Load and check for errors
sbml_reader = libsbml.SBMLReader()
sbml_document = sbml_reader.readSBML(sbml_file_new)
petab.is_sbml_consistent(sbml_document)
def convert_workflow(path, archive, archive_dir, sedml_doc=None):
with open(os.path.join(path, "info.json"), "r") as info_file:
wkfl_info = json.load(info_file)
model_path = os.path.join("/home/jovyan", wkfl_info['wkfl_model'])
# add model to archive as sbml file with .xml extension
sbml_document = convert_to_sbml(model_path.replace("/home/jovyan/", ""), write_to_file=False)
sbml_path, _ = get_unique_file_name(model_path.split('/').pop().split('.')[0]+".xml",
archive_dir.name)
with open(sbml_path, "w") as sbml_file:
sbml_file.write(libsbml.SBMLWriter().writeSBMLToString(sbml_document))
model_file = sbml_path.split('/').pop()
archive.addFile(sbml_path, "./{0}".format(model_file),
libcombine.KnownFormats.lookupFormat('sbml'), False)
# create Sed-ML document, name, and path
if sedml_doc is None:
sedml_doc = libsedml.SedDocument(1, 3)
sedml_document = convert_workflow_to_sedml(path, wkfl_info, model_file, sedml_doc)
sedml_name = os.path.dirname(path).split('/').pop().replace(".wkgp", ".xml")
sedml_path, _ = get_unique_file_name(sedml_name, archive_dir.name)
return {"doc":sedml_document, "name":sedml_name, "path":sedml_path}
return convert_workflow_to_sedml(path, wkfl_info, model_file, sedml_doc)
def main (args):
"""usage: flattenModel.py [-p] input-filename output-filename
-p : list unused ports
"""
if len(args) != 4 and len(args) != 3 :
print(main.__doc__)
sys.exit(1)
leavePorts = False
if len(args) == 3:
infile = args[1]
outfile = args[2]
elif len(args) == 4:
if args[1] != "-p":
print(main.__doc__)
sys.exit(1)
else:
leavePorts = True
infile = args[2]
outfile = args[3]
if not os.path.exists(infile):
print("[Error] %s : No such file." % (infile))
sys.exit(1)
reader = libsbml.SBMLReader()
writer = libsbml.SBMLWriter()
sbmldoc = reader.readSBML(infile)
if sbmldoc.getNumErrors() > 0:
if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
sbmldoc.printErrors()
elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
sbmldoc.printErrors()
else:
# Handle other error cases here.
sbmldoc.printErrors()
sys.exit(1)
# Create the converter options
props = libsbml.ConversionProperties()
props.addOption("flatten comp", True, "flatten comp")
props.addOption("leavePorts", leavePorts, "unused ports should be listed in the flattened model")
# do conversion
result = sbmldoc.convert(props)
if (result != libsbml.LIBSBML_OPERATION_SUCCESS):
sbmldoc.printErrors()
print("[Error] Conversion failed... ("+ str(result) + ")")
sys.exit(1)
writer.writeSBML(sbmldoc, outfile)
print("Flat model written to %s" % (outfile))
def write_sbmldoc_to_file(self, filename):
""" Writes the libsbml object as an SBML file.
Parameters
filename: a string with the name of the file to be written.
"""
writer = libsbml.SBMLWriter()
writer.writeSBML(self.sbml_obj, filename)
def main(args):
"""usage: convertFbcToCobra.py input-filename output-filename
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
infile = args[1]
outfile = args[2]
if not os.path.exists(infile):
print("[Error] %s : No such file." % infile)
sys.exit(1)
reader = libsbml.SBMLReader()
writer = libsbml.SBMLWriter()
sbmldoc = reader.readSBML(infile)
if sbmldoc.getNumErrors() > 0:
if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
sbmldoc.printErrors()
elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
sbmldoc.printErrors()
else:
# Handle other error cases here.
sbmldoc.printErrors()
# sys.exit(1)
# strip non-FBC plugins
for p_ in range(sbmldoc.getNumPlugins()):
if sbmldoc.getPlugin(p_).getPackageName() != 'fbc':
props = libsbml.ConversionProperties()
props.addOption(
"stripPackage", True,
"Strip SBML Level 3 package constructs from the model")
props.addOption("package",
sbmldoc.getPlugin(p_).getPackageName(),
"Name of the SBML Level 3 package to be stripped")
if sbmldoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS:
print("[Error] Failed to remove package: {}".format(
sbmldoc.getPlugin(p_).getPackageName()))
# convert to L2
props = libsbml.ConversionProperties()
props.addOption("convert fbc to cobra", True,
"Convert FBC model to Cobra model")
result = sbmldoc.convert(props)
if result != libsbml.LIBSBML_OPERATION_SUCCESS:
print("[Error] Conversion failed... (%d)" % result)
sys.exit(1)
writer.writeSBML(sbmldoc, outfile)
print("[OK] converted file %s to %s" % (infile, outfile))
def test_WriteL3SBML_error(self): d = libsbml.SBMLDocument() w = libsbml.SBMLWriter() self.assertEqual( False, w.writeSBML(d, "/tmp/impossible/path/should/fail") ) self.assert_( d.getNumErrors() == 1 ) self.assert_( d.getError(0).getErrorId() == libsbml.XMLFileUnwritable ) d = None w = None pass
def test_SBMLWriter_L3_setProgramVersion(self):
w = libsbml.SBMLWriter()
self.assert_( w != None )
i = w.setProgramVersion( "sss")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
i = w.setProgramVersion("")
self.assert_( i == libsbml.LIBSBML_OPERATION_SUCCESS )
_dummyList = [ w ]; _dummyList[:] = []; del _dummyList
pass
def modifyReleaseNumber(fileName):
print('modifying {0}'.format(fileName))
reader = libsbml.SBMLReader()
document = reader.readSBMLFromFile(fileName)
model = document.getModel()
species = model.getSpecies('S4')
species.setInitialAmount(species.getInitialConcentration())
species.unsetInitialConcentration()
writer = libsbml.SBMLWriter()
writer.writeSBMLToFile(document, fileName)
def reduceAnnotations(fileName):
sct, database, sbmlDocument = obtainSCT(fileName,
'config/reactionDefinitions.json',
False,
'config/namingConventions.json')
annotationDict, speciesNameDict = buildAnnotationDict(sbmlDocument)
buildAnnotationTree(annotationDict, sct, database)
speciesAnnotationsToSBML(sbmlDocument, annotationDict, speciesNameDict)
writer = libsbml.SBMLWriter()
return writer.writeSBMLToString(sbmlDocument)
def write_sbml(sbml_doc: libsbml.SBMLDocument, filename: str) -> None:
"""Write PEtab visualization table
Arguments:
sbml_doc: SBML document containing the SBML model
filename: Destination file name
"""
sbml_writer = libsbml.SBMLWriter()
ret = sbml_writer.writeSBMLToFile(sbml_doc, filename)
if not ret:
raise RuntimeError(f"libSBML reported error {ret} when trying to "
f"create SBML file {filename}.")
def write_sbml(
doc: libsbml.SBMLDocument,
filepath: Union[Path] = None,
program_name: str = None,
program_version: str = None,
validate: bool = False,
log_errors: bool = True,
units_consistency: bool = True,
modeling_practice: bool = True,
internal_consistency: bool = True,
) -> str:
"""Write SBMLDocument to file or string.
To write the SBML to string use 'filepath=None', which returns the SBML string.
Optional validation with validate flag.
:param doc: SBMLDocument to write
:param filepath: output file to write
:param validate: flag for validation (True: full validation, False: no validation)
:param program_name: Program name for SBML file
:param program_version: Program version for SBML file
:param log_errors: validation flag
:param units_consistency: validation flag
:param modeling_practice: validation flag
:param internal_consistency: validation flag
:return: None or SBML string
"""
writer = libsbml.SBMLWriter()
if program_name:
writer.setProgramName(program_name)
if program_version:
writer.setProgramVersion(program_version)
if filepath is None:
sbml_str = writer.writeSBMLToString(doc)
source = sbml_str
else:
writer.writeSBMLToFile(doc, str(filepath))
sbml_str = None
source = filepath
if validate:
validate_sbml(
source=source,
name=source,
log_errors=log_errors,
units_consistency=units_consistency,
modeling_practice=modeling_practice,
internal_consistency=internal_consistency,
)
return sbml_str # type: ignore
def writeModelToSBML(model, filepath):
"""
Write SBML Model to output file.
An empty SBMLDocument is created for the model.
:param model: SBML Model
:param filepath: output file path
:return:
"""
writer = libsbml.SBMLWriter()
doc = libsbml.SBMLDocument()
doc.setModel(model)
writer.writeSBMLToFile(doc, filepath)
def __getstate__(self):
state = self.__dict__.copy()
# libsbml stuff cannot be serialized directly
if self.sbml_model:
sbml_document = self.sbml_model.getSBMLDocument()
sbml_writer = libsbml.SBMLWriter()
state['sbml_string'] = sbml_writer.writeSBMLToString(sbml_document)
exclude = ['sbml_reader', 'sbml_document', 'sbml_model']
for key in exclude:
state.pop(key)
return state
def save_model(model, filename):
""" Save a model to an SBML file.
Arguments:
model (Model): model
filename (str): file path
"""
document = sb.SBMLDocument(DEFAULT_SBML_LEVEL, DEFAULT_SBML_VERSION)
sbml_model = document.createModel(model.id)
save_compartments(model, sbml_model)
save_metabolites(model, sbml_model)
save_reactions(model, sbml_model)
writer = sb.SBMLWriter()
writer.writeSBML(document, filename)
def expandAnnotation(fileName, bnglFile):
sct, database, sbmlDocument, _ = obtainSCT(
fileName, 'config/reactionDefinitions.json', False,
'config/namingConventions.json')
annotationDict, speciesNameDict = buildAnnotationDict(sbmlDocument)
buildAnnotationTree(annotationDict, sct, database)
speciesAnnotationsToSBML(sbmlDocument, annotationDict, speciesNameDict)
#species, rules, par = createDataStructures(bnglFile)
#reactionAnnotationDict = buildReactionAnnotationDict(rules)
#reactionAnnotationsToSBML(sbmlDocument,reactionAnnotationDict)
#reactionAnnotationsToSBML(sbmlDocument,reactionAnnotation)
#reactionAnnotationsToSBML(sbmlDocument)
writer = libsbml.SBMLWriter()
return writer.writeSBMLToString(sbmlDocument)
def compile_model(self):
"""
Compile the model. If the output folder exists already, it is first
deleted.
"""
# check prerequisites
if not petab.condition_table_is_parameter_free(
self.petab_problem.condition_df):
raise AssertionError(
"Parameter dependent conditions in the condition file "
"are not yet supported.")
# delete output directory
if os.path.exists(self.output_folder):
shutil.rmtree(self.output_folder)
# constant parameters
condition_columns = self.petab_problem.condition_df.columns.values
constant_parameter_ids = list(
set(condition_columns) - {'conditionId', 'conditionName'})
# observables
observables = self.petab_problem.get_observables()
# sigmas
sigmas = self.petab_problem.get_sigmas(remove=True)
# noise distributions
noise_distrs = _to_amici_noise_distributions(
self.petab_problem.get_noise_distributions())
# model to string
sbml_string = libsbml.SBMLWriter().writeSBMLToString(
self.petab_problem.sbml_document)
# init sbml importer
sbml_importer = amici.SbmlImporter(sbml_string, from_file=False)
# convert
sbml_importer.sbml2amici(modelName=self.model_name,
output_dir=self.output_folder,
observables=observables,
constantParameters=constant_parameter_ids,
sigmas=sigmas,
noise_distributions=noise_distrs)
def main(args):
"""usage: stripPackage.py input-filename package-to-strip output-filename
"""
if len(args) != 4:
print(main.__doc__)
sys.exit(1)
infile = args[1]
package = args[2]
outfile = args[3]
if not os.path.exists(infile):
print("[Error] %s : No such file." % (infile))
sys.exit(1)
reader = libsbml.SBMLReader()
writer = libsbml.SBMLWriter()
sbmldoc = reader.readSBML(infile)
if sbmldoc.getNumErrors() > 0:
if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
sbmldoc.printErrors()
elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
sbmldoc.printErrors()
else:
# Handle other error cases here.
sbmldoc.printErrors()
sys.exit(1)
props = libsbml.ConversionProperties()
props.addOption("stripPackage", True,
"Strip SBML Level 3 package constructs from the model")
props.addOption("package", package,
"Name of the SBML Level 3 package to be stripped")
if (sbmldoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS):
print("[Error] Conversion failed...")
sys.exit(1)
writer.writeSBML(sbmldoc, outfile)
print("[OK] stripped package '%s' from %s to %s" %
(package, infile, outfile))
def main(args):
"""usage: flattenArrays.py input-filename output-filename
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
infile = args[1]
outfile = args[2]
if not os.path.exists(infile):
print("[Error] {} : No such file.".format(infile))
sys.exit(1)
reader = libsbml.SBMLReader()
writer = libsbml.SBMLWriter()
sbmldoc = reader.readSBML(infile)
if sbmldoc.getNumErrors() > 0:
if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
sbmldoc.printErrors()
elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
sbmldoc.printErrors()
else:
# Handle other error cases here.
sbmldoc.printErrors()
sys.exit(1)
props = libsbml.ConversionProperties()
props.addOption("flatten arrays", True, "flatten arrays")
# Optional: validate flattened file ... may take some time
# props.addOption("performValidation", True, "perform validation before and after trying to flatten")
result = sbmldoc.convert(props)
if (result != libsbml.LIBSBML_OPERATION_SUCCESS):
print("[Error] Array flattening failed... ({})".format(result))
sys.exit(1)
writer.writeSBML(sbmldoc, outfile)
print("[OK] Flattened arrays file {} to {}".format(infile, outfile))
def main(args):
"""usage: convertFbcToCobra.py input-filename output-filename
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
infile = args[1]
outfile = args[2]
if not os.path.exists(infile):
print("[Error] %s : No such file." % (infile))
sys.exit(1)
reader = libsbml.SBMLReader()
writer = libsbml.SBMLWriter()
sbmldoc = reader.readSBML(infile)
if sbmldoc.getNumErrors() > 0:
if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
sbmldoc.printErrors()
elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
sbmldoc.printErrors()
else:
# Handle other error cases here.
sbmldoc.printErrors()
#sys.exit(1)
props = libsbml.ConversionProperties()
props.addOption("convert fbc to cobra", True,
"Convert FBC model to Cobra model")
result = sbmldoc.convert(props)
if (result != libsbml.LIBSBML_OPERATION_SUCCESS):
print("[Error] Conversion failed... (%d)" % (result))
sys.exit(1)
writer.writeSBML(sbmldoc, outfile)
print("[OK] converted file %s to %s" % (infile, outfile))
def main(args):
"""usage: promoteParameters.py input-filename output-filename
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
infile = args[1]
outfile = args[2]
if not os.path.exists(infile):
print("[Error] %s : No such file." % (infile))
sys.exit(1)
reader = libsbml.SBMLReader()
writer = libsbml.SBMLWriter()
sbmldoc = reader.readSBML(infile)
if sbmldoc.getNumErrors() > 0:
if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
sbmldoc.printErrors()
elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
sbmldoc.printErrors()
else:
# Handle other error cases here.
sbmldoc.printErrors()
sys.exit(1)
props = libsbml.ConversionProperties()
props.addOption("promoteLocalParameters", True,
"Promotes all Local Parameters to Global ones")
if (sbmldoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS):
print("[Error] Conversion failed...")
sys.exit(1)
writer.writeSBML(sbmldoc, outfile)
print("[OK] wrote %s" % (package, infile, outfile))
def main (args):
"""usage: inlineFunctionDefinitions.py input-filename output-filename
"""
if len(args) != 3:
print(main.__doc__)
sys.exit(1)
infile = args[1]
outfile = args[2]
if not os.path.exists(infile):
print("[Error] %s : No such file." % infile)
sys.exit(1)
reader = libsbml.SBMLReader()
writer = libsbml.SBMLWriter()
sbmldoc = reader.readSBML(infile)
if sbmldoc.getNumErrors() > 0:
if sbmldoc.getError(0).getErrorId() == libsbml.XMLFileUnreadable:
# Handle case of unreadable file here.
sbmldoc.printErrors()
elif sbmldoc.getError(0).getErrorId() == libsbml.XMLFileOperationError:
# Handle case of other file error here.
sbmldoc.printErrors()
else:
# Handle other error cases here.
sbmldoc.printErrors()
sys.exit(1)
props = libsbml.ConversionProperties()
props.addOption("expandFunctionDefinitions", True)
if sbmldoc.convert(props) != libsbml.LIBSBML_OPERATION_SUCCESS:
print("[Error] Conversion failed...")
sys.exit(1)
writer.writeSBML(sbmldoc, outfile)
print("[OK] wrote {}".format(outfile))
def save_network_to_file(net, filename):
sbml_document = SbmlSaver.network_to_sbml(net)
s = libsbml.SBMLWriter()
s.writeSBMLToFile(sbml_document, filename)
def save(self, outfile):
"""
Save the current working SPN to a file of a given name
in the current dir. vdict contains the labels and data
of the vector vars, mdict is the matrices.
(Note on SBML version compatibility:
SBML output is written for Level 3 Version 1, but has no
errors with any Level 2 versions. 6 Errors occur with an L1
compatibility check if non-integer rates are used.)
"""
import re
import libsbml as lb
# build SBML document and header
f = open(outfile, 'w')
lev = 3
ver = 1
out = lb.SBMLDocument(lev,ver)
model = out.createModel()
model.setId('StochasticPetriNet')
# Build file body
cell = model.createCompartment()
cell.setId('Cell')
# Causes an error if omitted in earlier levels of SBML
cell.setSpatialDimensions(3)
model.addCompartment(cell)
c1 = 0 # places count
pdict = {}
c2 = 0 # trans count?
for spe in self.vdict['p']:
s = model.createSpecies()
s.setId(spe)
pdict[c1] = spe
s.setCompartment(cell.getId())
s.setInitialAmount(int(self.vdict['m'][c1]))
model.addSpecies(s)
c1 += 1
for reac in self.vdict['t']:
r = model.createReaction()
r.setId(reac)
kl = r.createKineticLaw()
# Get 'rate' params, insert into KineticLaw local param field
lp = kl.createLocalParameter()
lp.setValue(self.vdict['r'][c2])
lp.setId('rate' + str(c2))
model.addReaction(r)
# Use pre matrix to write named reactants & stoichiometries
for bin in self.mdict['pre'][c2]:
# For each place
for q in range(0, c1):
if bin[0,q] != 0 :
t = model.createReactant()
t.setSpecies(self.vdict['p'][q])
# Convert type numpy.int64 -> int
t.setStoichiometry(int(bin[0,q]))
# Same for post matrix
for bon in self.mdict['post'][c2]:
# For each place
for t in range(0, c1):
if bon[0,t] != 0 :
p = model.createProduct()
p.setSpecies(self.vdict['p'][t])
# Convert type numpy.int64 -> int
p.setStoichiometry(int(bon[0,t]))
c2+=1
## Compatibility checks
# Uncomment print statements to view errors
print '\t1.0 err: ', out.checkL1Compatibility()
# print out.printErrors()
print '\t2.1 err: ', out.checkL2v1Compatibility()
# print out.printErrors()
print '\t2.2 err: ', out.checkL2v2Compatibility()
# print out.printErrors()
print '\t2.3 err: ', out.checkL2v3Compatibility()
# print out.printErrors()
print '\t2.4 err: ', out.checkL2v4Compatibility()
# print out.printErrors()
print '\t3.1 err: ', out.checkL3v1Compatibility()
# write to file
w = lb.SBMLWriter()
w.setProgramName('SPNlib')
w.setProgramVersion('1.0')
w.writeSBML(out, outfile)
def writeSBML(document, fileName):
writer = libsbml.SBMLWriter()
writer.writeSBMLToFile(document, fileName)
for idx, row in enumerate(species_sheet[1:]):
Annot = ""
for col in range(4, (len(row))):
aa = str(row[col].strip())
if aa == "nan" or aa == "":
break
else:
Annot = Annot + " " + row[col]
sbml_model.getSpecies(row[0]).setAnnotation(Annot)
# Set compartment annotations
for row in compartment_sheet[1:]:
sbml_model.getCompartment(row[0]).setAnnotation(row[2])
# Write with the same name or use the next section instead of below lines
writer = libsbml.SBMLWriter()
writer.writeSBML(sbml_doc, sbml_file)
# # Change model name and write with a new name
# sbml_model.setName(model_name+'_Annot')
# sbml_model.setId(model_name+'_Annot')
# sbml_filewAnnot = model_name+'_Annot.xml'
# writer = libsbml.SBMLWriter()
# writer.writeSBML(sbml_doc, sbml_filewAnnot)
# sbml_file = sbml_filewAnnot # Comment-out to use the file name w/t annotations
model_name = sbml_file[0:-4]
model_output_dir = model_name
sbml_reader = libsbml.SBMLReader()
sbml_doc = sbml_reader.readSBML(sbml_file)