def add_species_to_model(self, reagent):
if reagent not in self.seen_reagents:
species = self.model.createSpecies()
name = ExpandGraph.node_name(self.graph, reagent)
name = self.replace_non_alphanumeric_with_underscore(name)
SBMLGenerator.check(species.setId(name), 'set species id')
self.seen_reagents.add(reagent)
def add_reaction(self, reaction):
_, _, reversibility = reaction
current_reaction = self.model.createReaction()
reaction_name = ExpandGraph.human_readable_reaction(self.graph, reaction)
reaction_name = self.replace_non_alphanumeric_with_underscore(reaction_name)
SBMLGenerator.check(current_reaction.setId(reaction_name), 'set reaction id')
SBMLGenerator.check(current_reaction.setReversible(reversibility), 'set reaction reversibility flag')
return current_reaction
def test_generate_empty_stoichiometric_matrix_size_43(self):
g = nx.DiGraph()
g.add_nodes_from([1, 2, 3, 4])
g.add_edge(1, 2)
n_of_rows = len(g.nodes())
n_of_columns = 3 * len(g.edges())
lead = ExpandGraph.generate_empty_stoichiometric_matrix(
n_of_rows, n_of_columns)
gold = [[0, 0, 0], [0, 0, 0], [0, 0, 0], [0, 0, 0]]
assert lead == gold
def export_efm_human_readable():
with open('result/EFM_human.txt', 'w') as f:
f.write("Total number of EFMs: {}\n".format(len(r.result)))
for i, efms in enumerate(r.result, start=1):
f.write('EFM #{}\n'.format(str(i)))
for index, reaction in enumerate(efms):
if reaction == 1:
f.write('{}\n'.format(
ExpandGraph.human_readable_reaction(
expanded_graph.graph,
expanded_graph.reactions[index])))
f.write('\n')
def add_species_to_reaction(self, reagent, reaction_reference):
name = ExpandGraph.node_name(self.graph, reagent)
name = GenerateSBML.replace_non_alphanumeric_with_underscore(name)
SBMLGenerator.check(reaction_reference.setSpecies(name), 'assign species')
def test_generate_empty_stoichiometric_matrix_size_00(self):
lead = ExpandGraph.generate_empty_stoichiometric_matrix(0, 0)
gold = list()
assert lead == gold
def test_generate_empty_stoichiometric_matrix_size_11(self):
lead = ExpandGraph.generate_empty_stoichiometric_matrix(1, 1)
gold = [[0]]
assert lead == gold
f.write(str(expanded_graph.reactions[index]))
f.write('\n')
f.write('\n')
def export_sbml(graph, reactions):
document = GenerateSBML(graph, reactions=reactions).generate_sbml()
with open('result/stoichiometric_matrix_in_SBML.xml', "w") as f:
f.write(SBMLGenerator.convert_to_xml(document=document))
if __name__ == '__main__':
parser = pars()
args = parser.parse_args()
graph = GraphReader(args.edge_list).create_graph()
expanded_graph = ExpandGraph(graph)
print("I've deleted rows %s with all zeroes" %
expanded_graph.deleted_rows_count)
export_stoichiometric_matrix()
export_reactions_human_readable()
# feed stoichiometric matrix and reaction vector to EFM Sampler
r = Sampler(expanded_graph.matrix, expanded_graph.vector)
nx.write_graphml(graph, "result/imported_graph.graphml")
nx.write_graphml(expanded_graph.graph, "result/expanded_graph.graphml")
export_sbml(expanded_graph.graph, expanded_graph.reactions)
export_efm_human_readable()
export_efm_reaction_numbers()
# print expanded_graph.vector