def create_model(output_dir):
""" Create all submodels and comp model.
:param output_dir: results directory
:rtype:
:return directory in which model files exist.
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
f_annotations = os.path.join(os.path.dirname(os.path.abspath(__file__)),
settings.ANNOTATIONS_LOCATION)
annotations = annotator.ModelAnnotator.read_annotations(f_annotations)
# create sbml
doc_fba = fba_model(settings.FBA_LOCATION, directory, annotations=annotations)
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba, annotations=annotations)
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba, annotations=annotations)
emds = {
"{}_fba".format(settings.MODEL_ID): settings.FBA_LOCATION,
"{}_bounds".format(settings.MODEL_ID): settings.BOUNDS_LOCATION,
"{}_update".format(settings.MODEL_ID): settings.UPDATE_LOCATION,
}
# flatten top model
top_model(settings.TOP_LOCATION, directory, emds, doc_fba, annotations=annotations)
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory, settings.FLATTENED_LOCATION))
# create reports
locations = [
settings.FBA_LOCATION,
settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION,
settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_reports(sbml_paths, directory, validate=False)
# create sedml
from sbmlutils.dfba.sedml import create_sedml
species_ids = ", ".join(['A', 'C', 'D'])
reaction_ids = ", ".join(['R4', 'EX_A', 'EX_C'])
create_sedml(settings.SEDML_LOCATION, settings.TOP_LOCATION, directory=directory,
dt=0.1, tend=50, species_ids=species_ids, reaction_ids=reaction_ids)
return directory
def create_model(output_dir):
""" Create all models.
:return: directory where SBML files are located
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
print("FBA")
doc_fba = fba_model(settings.FBA_LOCATION, directory)
print("BOUNDS")
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba)
print("UPDATE")
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba)
emds = {
"{}_fba".format(settings.MODEL_ID): settings.FBA_LOCATION,
"{}_bounds".format(settings.MODEL_ID): settings.BOUNDS_LOCATION,
"{}_update".format(settings.MODEL_ID): settings.UPDATE_LOCATION,
}
print("TOP")
top_model(settings.TOP_LOCATION,
directory,
emds,
doc_fba=doc_fba,
validate=True)
# flatten top model
print("FLATTENING")
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory,
settings.FLATTENED_LOCATION))
# create report
locations = [
settings.FBA_LOCATION, settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION, settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_reports(sbml_paths, directory, validate=False)
return directory
def model_reports(biomodels_folder, reports_folder):
""" Create sbmlreports for all biomodels.
:return:
"""
#if not os.path.exists(reports_folder):
# os.mkdir(reports_folder)
# get all SBML files
sbml_paths = []
for f in os.listdir(biomodels_folder):
if f.endswith('.xml'):
f_path = os.path.join(biomodels_folder, f)
if os.path.isfile(f_path):
sbml_paths.append(f_path)
pprint(sbml_paths)
sbmlreport.create_reports(sorted(sbml_paths)[:10],
output_dir=reports_folder,
validate=False)
def create_model(output_dir):
""" Create all models.
:return: directory where SBML files are located
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
# create sbml
import time
t_start = time.time()
doc_fba = fba_model(settings.FBA_LOCATION, directory)
t_fba = time.time()
print('{:<10}: {:3.2f}'.format('fba', t_fba - t_start))
bounds_model(settings.BOUNDS_LOCATION, directory, doc_fba=doc_fba)
t_bounds = time.time()
print('{:<10}: {:3.2f}'.format('bounds', t_bounds - t_fba))
update_model(settings.UPDATE_LOCATION, directory, doc_fba=doc_fba)
t_update = time.time()
print('{:<10}: {:3.2f}'.format('update', t_update - t_bounds))
emds = {
"ecoli_fba": settings.FBA_LOCATION,
"ecoli_bounds": settings.BOUNDS_LOCATION,
"ecoli_update": settings.UPDATE_LOCATION,
}
# flatten top model
top_model(settings.TOP_LOCATION, directory, emds, doc_fba=doc_fba)
t_top = time.time()
print('{:<10}: {:3.2f}'.format('top', t_top - t_update))
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory,
settings.FLATTENED_LOCATION))
t_flat = time.time()
print('{:<10}: {:3.2f}'.format('flat', t_flat - t_top))
# create reports
locations = [
settings.FBA_LOCATION, settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION, settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_reports(sbml_paths, directory, validate=False)
# create sedml
from sbmlutils.dfba.sedml import create_sedml
sids = [
'ac_e', 'acald_e', 'akg_e', 'co2_e', 'etoh_e', 'for_e', 'fru_e',
'fum_e', 'glc__D_e', 'gln__L_e', 'glu__L_e', 'h_e', 'h2o_e',
'lac__D_e', 'mal__L_e', 'nh4_e', 'o2_e', 'pi_e', 'pyr_e', 'succ_e', 'X'
]
species_ids = ", ".join(sids)
reaction_ids = ", ".join(['EX_{}'.format(sid) for sid in sids])
create_sedml(settings.SEDML_LOCATION,
settings.TOP_LOCATION,
directory=directory,
dt=0.01,
tend=3.5,
species_ids=species_ids,
reaction_ids=reaction_ids)
return directory
def create_model(output_dir):
""" Create all models.
:return:
"""
directory = utils.versioned_directory(output_dir, version=settings.VERSION)
f_annotations = os.path.join(os.path.dirname(os.path.abspath(__file__)),
settings.ANNOTATIONS_LOCATION)
annotations = annotator.ModelAnnotator.read_annotations(f_annotations)
# create sbml
doc_fba = fba_model(settings.FBA_LOCATION,
directory,
annotations=annotations)
bounds_model(settings.BOUNDS_LOCATION,
directory,
doc_fba=doc_fba,
annotations=annotations)
update_model(settings.UPDATE_LOCATION,
directory,
doc_fba=doc_fba,
annotations=annotations)
emds = {
"diauxic_fba": settings.FBA_LOCATION,
"diauxic_bounds": settings.BOUNDS_LOCATION,
"diauxic_update": settings.UPDATE_LOCATION,
}
top_model(settings.TOP_LOCATION,
directory,
emds,
doc_fba=doc_fba,
annotations=annotations)
# flatten top model
comp.flattenSBMLFile(sbml_path=pjoin(directory, settings.TOP_LOCATION),
output_path=pjoin(directory,
settings.FLATTENED_LOCATION))
# create reports
locations = [
settings.FBA_LOCATION, settings.BOUNDS_LOCATION,
settings.UPDATE_LOCATION, settings.TOP_LOCATION,
settings.FLATTENED_LOCATION
]
sbml_paths = [pjoin(directory, fname) for fname in locations]
sbmlreport.create_reports(sbml_paths, directory, validate=False)
# create sedml
from sbmlutils.dfba.sedml import create_sedml
species_ids = ", ".join(['Ac', 'Glcxt', 'O2', 'X'])
reaction_ids = ", ".join(
['vO2_transfer', 'EX_Ac', 'EX_Glcxt', 'EX_O2', 'EX_X'])
create_sedml(settings.SEDML_LOCATION,
settings.TOP_LOCATION,
directory=directory,
dt=0.01,
tend=15,
species_ids=species_ids,
reaction_ids=reaction_ids)
return directory
