def write_product(directory=None, information=None):
"""
Writes product information to file
arguments:
directory (str): directory for product files
information (object): information to write to file
raises:
returns:
"""
# Specify directories and files.
path = os.path.join(directory, "network")
utility.confirm_path_directory(path)
path_nodes_reactions = os.path.join(path, "nodes_reactions.pickle")
path_nodes_metabolites = os.path.join(path, "nodes_metabolites.pickle")
path_links = os.path.join(path, "links.pickle")
# Write information to file.
with open(path_nodes_reactions, "wb") as file_product:
pickle.dump(information["nodes_reactions"], file_product)
with open(path_nodes_metabolites, "wb") as file_product:
pickle.dump(information["nodes_metabolites"], file_product)
with open(path_links, "wb") as file_product:
pickle.dump(information["links"], file_product)
def write_product(directory=None, information=None):
"""
Writes product information to file
arguments:
directory (str): directory for product files
information (object): information to write to file
raises:
returns:
"""
# Specify directories and files.
path = os.path.join(directory, "extraction")
utility.confirm_path_directory(path)
path_pickle = os.path.join(path, "hmdb_summary.pickle")
path_text = os.path.join(path, "hmdb_summary.tsv")
# Write information to file.
with open(path_pickle, "wb") as file_product:
pickle.dump(information["summary_object"], file_product)
utility.write_file_table(
information=information["summary_list"],
path_file=path_text,
names=information["summary_list"][0].keys(),
delimiter="\t"
)
def write_product(directory=None, information=None):
"""
Writes product information to file
arguments:
directory (str): directory for product files
information (object): information to write to file
raises:
returns:
"""
# Specify directories and files.
path = os.path.join(directory, "model")
utility.confirm_path_directory(path)
path_dymetabonet = os.path.join(path, "dymetabonet.json")
path_compartments = os.path.join(path, "compartments.pickle")
path_processes = os.path.join(path, "processes.pickle")
path_reactions = os.path.join(path, "reactions.pickle")
path_metabolites = os.path.join(path, "metabolites.pickle")
path_compartments_text = os.path.join(path, "compartments.tsv")
path_processes_text = os.path.join(path, "processes.tsv")
path_reactions_text = os.path.join(path, "reactions.tsv")
path_metabolites_text = os.path.join(path, "metabolites.tsv")
# Write information to file.
with open(path_dymetabonet, "w") as file_product:
json.dump(information["dymetabonet"], file_product)
with open(path_compartments, "wb") as file_product:
pickle.dump(information["compartments"], file_product)
with open(path_processes, "wb") as file_product:
pickle.dump(information["processes"], file_product)
with open(path_reactions, "wb") as file_product:
pickle.dump(information["reactions"], file_product)
with open(path_metabolites, "wb") as file_product:
pickle.dump(information["metabolites"], file_product)
utility.write_file_table(information=information["compartments_text"],
path_file=path_compartments_text,
names=information["compartments_text"][0].keys(),
delimiter="\t")
utility.write_file_table(information=information["processes_text"],
path_file=path_processes_text,
names=information["processes_text"][0].keys(),
delimiter="\t")
utility.write_file_table(information=information["reactions_text"],
path_file=path_reactions_text,
names=information["reactions_text"][0].keys(),
delimiter="\t")
utility.write_file_table(information=information["metabolites_text"],
path_file=path_metabolites_text,
names=information["metabolites_text"][0].keys(),
delimiter="\t")
def write_product(directory=None, information=None):
"""
Writes product information to file
arguments:
directory (str): directory for product files
information (object): information to write to file
raises:
returns:
"""
# Specify directories and files.
path = os.path.join(directory, "reconciliation")
utility.confirm_path_directory(path)
path_file = os.path.join(path, "recon2m2_reconciliation.xml")
# Write information to file.
information.write(path_file, xml_declaration=False)
def write_product(directory=None, information=None):
"""
Writes product information to file
arguments:
directory (str): directory for product files
information (object): information to write to file
raises:
returns:
"""
# Specify directories and files.
path_network = os.path.join(directory, "network")
path = os.path.join(path_network, "measurement")
utility.confirm_path_directory(path)
path_pickle = os.path.join(path, "metabolites.pickle")
path_metabolites_text = os.path.join(path, "metabolites.tsv")
path_reactions_text = os.path.join(path, "reactions.tsv")
# Write information to file.
with open(path_pickle, "wb") as file_product:
pickle.dump(information["metabolites_measurement"], file_product)
utility.write_file_table(
information=information["metabolites_measurement_text"],
path_file=path_metabolites_text,
names=information["metabolites_measurement_text"][0].keys(),
delimiter="\t"
)
if False:
utility.write_file_table(
information=information["reactions_measurement_text"],
path_file=path_reactions_text,
names=information["reactions_measurement_text"][0].keys(),
delimiter="\t"
)
def write_product(directory=None, information=None):
"""
Writes product information to file
arguments:
directory (str): directory for product files
information (object): information to write to file
raises:
returns:
"""
# Specify directories and files.
path = os.path.join(directory, "network")
utility.confirm_path_directory(path)
path_networkx = os.path.join(path, "network_networkx.pickle")
path_cytoscape = os.path.join(path, "network_cytoscape.json")
# Write information to file.
with open(path_networkx, "wb") as file_product:
pickle.dump(information["networkx"], file_product)
with open(path_cytoscape, "w") as file_product:
json.dump(information["cytoscape"], file_product)
