def save_model_to_file(model, filename):
""" Save a model to a file based on the extension of the file name.
Parameters
----------
model : cobra.core.Model
Model object loaded from file
filename : str
Path to model file
Raises
------
IOError
If model file extension is not supported.
"""
(root, ext) = splitext(filename)
if ext == '.mat':
save_matlab_model(model, filename)
elif ext == '.xml' or ext == '.sbml':
write_sbml_model(model, filename)
elif ext == '.json':
save_json_model(model, filename)
else:
raise IOError(
'Model file extension not supported for {0}'.format(filename))
return
def test_mat_read_write(self):
test_output_filename = "test_mat_write.mat"
io.save_matlab_model(self.model, test_output_filename)
reread = io.load_matlab_model(test_output_filename)
self.assertEqual(len(self.model.reactions), len(reread.reactions))
self.assertEqual(len(self.model.metabolites), len(reread.metabolites))
for i in range(len(self.model.reactions)):
self.assertEqual(len(self.model.reactions[i]._metabolites), len(reread.reactions[i]._metabolites))
self.assertEqual(self.model.reactions[i].id, reread.reactions[i].id)
unlink(test_output_filename)
def test_save_matlab_model(tmpdir, mini_model, raven_model):
"""Test the writing of MAT model."""
mini_output_file = tmpdir.join("mini.mat")
raven_output_file = tmpdir.join("raven.mat")
# scipy.io.savemat() doesn't support anything other than
# str or file-stream object, hence the str conversion
io.save_matlab_model(mini_model, str(mini_output_file))
io.save_matlab_model(raven_model, str(raven_output_file))
assert mini_output_file.check()
assert raven_output_file.check()
def test_save_matlab_model(tmpdir, mini_model, raven_model):
"""Test the writing of MAT model."""
mini_output_file = tmpdir.join("mini.mat")
raven_output_file = tmpdir.join("raven.mat")
# scipy.io.savemat() doesn't support anything other than
# str or file-stream object, hence the str conversion
io.save_matlab_model(mini_model, str(mini_output_file))
io.save_matlab_model(raven_model, str(raven_output_file))
assert mini_output_file.check()
assert raven_output_file.check()
def test_mat_read_write(self):
from warnings import catch_warnings
test_output_filename = join(gettempdir(), "test_mat_write.mat")
io.save_matlab_model(self.model, test_output_filename)
with catch_warnings(record=True) as w:
reread = io.load_matlab_model(test_output_filename)
self.assertEqual(len(self.model.reactions), len(reread.reactions))
self.assertEqual(len(self.model.metabolites), len(reread.metabolites))
for i in range(len(self.model.reactions)):
self.assertEqual(len(self.model.reactions[i]._metabolites), \
len(reread.reactions[i]._metabolites))
self.assertEqual(self.model.reactions[i].id, reread.reactions[i].id)
unlink(test_output_filename)
def test_mat_read_write(self):
"""read and write COBRA toolbox models in .mat files"""
from warnings import catch_warnings
test_output_filename = join(gettempdir(), "test_mat_write.mat")
io.save_matlab_model(self.model, test_output_filename)
with catch_warnings(record=True) as w:
reread = io.load_matlab_model(test_output_filename)
self.assertEqual(len(self.model.reactions), len(reread.reactions))
self.assertEqual(len(self.model.metabolites), len(reread.metabolites))
for i in range(len(self.model.reactions)):
self.assertEqual(len(self.model.reactions[i]._metabolites), \
len(reread.reactions[i]._metabolites))
self.assertEqual(self.model.reactions[i].id,
reread.reactions[i].id)
unlink(test_output_filename)
def mvgem(input_model, output_model):
"""Convert GEM format INPUT_MODEL to OUTPUT_MODEL.
The format will be infered based on the extension of OUTPUT_MODEL.
Supported formats: .sbml, .xml, .json, .mat
"""
model = load_model(input_model)
out_format = get_destination_format(output_model)
if out_format == "SBML":
write_sbml_model(model, output_model)
elif out_format == "MAT":
save_matlab_model(model, output_model)
elif out_format == "JSON":
save_json_model(model, output_model)
else:
click.BadParameter(
"Output format %s could not be recognised" % out_format
).show()
mini.reactions.get_by_id(i).lower_bound = mini.reactions.PGI.lower_bound
# set names and annotation
for g in mini.genes:
try:
tg = textbook.genes.get_by_id(g.id)
except KeyError:
continue
g.name = tg.name
g.annotation = tg.annotation
mini.reactions.sort()
mini.genes.sort()
mini.metabolites.sort()
# output to various formats
with open("mini.pickle", "wb") as outfile:
dump(mini, outfile, protocol=2)
save_matlab_model(mini, "mini.mat")
save_json_model(mini, "mini.json", pretty=True)
write_sbml_model(mini, "mini_fbc2.xml")
write_sbml_model(mini, "mini_fbc2.xml.bz2")
write_sbml_model(mini, "mini_fbc2.xml.gz")
write_sbml2(mini, "mini_fbc1.xml", use_fbc_package=True)
write_sbml_model(mini, "mini_cobra.xml", use_fbc_package=False)
# fva results
fva_result = cobra.flux_analysis.flux_variability_analysis(textbook)
clean_result = OrderedDict()
for key in sorted(fva_result):
clean_result[key] = {k: round(v, 5) for k, v in fva_result[key].items()}
with open("textbook_fva.json", "w") as outfile:
json_dump(clean_result, outfile)
def raise_scipy_errors():
with pytest.raises(ImportError):
io.save_matlab_model(None, 'test')
with pytest.raises(ImportError):
io.load_matlab_model('test')
mini.reactions.get_by_id(i).lower_bound = mini.reactions.PGI.lower_bound
# set names and annotation
for g in mini.genes:
try:
tg = textbook.genes.get_by_id(g.id)
except KeyError:
continue
g.name = tg.name
g.annotation = tg.annotation
mini.reactions.sort()
mini.genes.sort()
mini.metabolites.sort()
# output to various formats
with open("mini.pickle", "wb") as outfile:
dump(mini, outfile, protocol=2)
save_matlab_model(mini, "mini.mat")
save_json_model(mini, "mini.json", pretty=True)
write_sbml_model(mini, "mini_fbc2.xml")
write_sbml_model(mini, "mini_fbc2.xml.bz2")
write_sbml_model(mini, "mini_fbc2.xml.gz")
write_sbml2(mini, "mini_fbc1.xml", use_fbc_package=True)
write_sbml_model(mini, "mini_cobra.xml", use_fbc_package=False)
raven = load_matlab_model("raven.mat")
with open("raven.pickle", "wb") as outfile:
dump(raven, outfile, protocol=2)
# fva results
fva_result = cobra.flux_analysis.flux_variability_analysis(textbook)
clean_result = OrderedDict()
for key in sorted(fva_result):
clean_result[key] = {k: round(v, 5) for k, v in fva_result[key].items()}
from cobra.test import create_test_model
model_names = ['salmonella', 'iJO1366', 'Yersinia_pestis_CO92_iPC815']
for model_name in model_names:
# read in old pickle and model from sbml
model_pickle = model_name + '.pickle'
if model_name == "iJO1366":
new_model = read_legacy_sbml(model_name + '.xml')
else:
new_model = read_sbml_model(model_name + '.xml')
# update other attributes
if isfile(model_name + ".genes"):
with open(model_name + ".genes", "rb") as infile:
gene_names = load(infile)
for gene in new_model.genes:
gene.name = gene_names[gene.id]
if isfile(model_name + ".media"):
with open(model_name + ".media", "rb") as infile:
new_model.media_compositions = load(infile)
new_model._cobra_version = get_version()
# write out new pickle
with open(model_pickle, 'wb') as outfile:
dump(new_model, outfile, protocol=2)
# write out other formats for iJO1366
if model_name == "iJO1366":
save_matlab_model(new_model, model_name + ".mat")
save_json_model(new_model, model_name + ".json")
if model_name == "salmonella":
write_sbml_model(new_model, model_name + "_fbc.xml")
def raise_scipy_errors():
with pytest.raises(ImportError):
io.save_matlab_model(None, 'test')
with pytest.raises(ImportError):
io.load_matlab_model('test')