def write_product(directory, information):
# Specify directories and files
path_compartments = directory + 'compartments.pickle'
path_processes = directory + 'processes.pickle'
path_reactions = directory + 'reactions.pickle'
path_metabolites = directory + 'metabolites.pickle'
path_metabolites_report = directory + 'metabolites.tsv'
path_reactions_report = directory + 'reactions.tsv'
# Write information to file.
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)
write_file_table(information=information['metabolites_report'],
path_file=path_metabolites_report,
names=information['metabolites_report'][0].keys(),
delimiter='\t')
write_file_table(information=information['reactions_report'],
path_file=path_reactions_report,
names=information['reactions_report'][0].keys(),
delimiter='\t')
def write_product(directory, information):
# Specify directories and files
path_pickle = directory + 'hmdb_summary.pickle'
path_text = directory + 'hmdb_summary.tsv'
# Write information to file
with open(path_pickle, 'wb') as file_product:
pickle.dump(information['summary_object'], file_product)
write_file_table(information=information['summary_list'],
path_file=path_text,
names=information['summary_list'][0].keys(),
delimiter='\t')
def write_product(directory, information):
# Specify directories and files
path_compartments = directory + "compartments.pickle"
path_processes = directory + "processes.pickle"
path_reactions = directory + "reactions.pickle"
path_reactions_summary = directory + "reactions_summary.tsv"
path_metabolites = directory + "metabolites.pickle"
path_metabolites_report = directory + "metabolites.tsv"
path_reactions_report = directory + "reactions.tsv"
# Write information to file
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)
try:
write_file_table(information=information["metabolites_report"],
path_file=path_metabolites_report,
names=information["metabolites_report"][0].keys(),
delimiter="\t")
write_file_table(information=information["reactions_report"],
path_file=path_reactions_report,
names=information["reactions_report"][0].keys(),
delimiter="\t")
except:
write_file_table(information=information["reactions_summary"],
path_file=path_reactions_summary,
names=information["reactions_summary"][0].keys(),
delimiter="\t")
def write_product(directory, information, final_directory):
# Specify directories and files
path_dymetabonet = directory + dymetabonet
final_dymetabonet = final_directory + dymetabonet
path_compartments = directory + compartment_pickle
path_processes = directory + process_pickle
path_reactions = directory + reaction_pickle
path_metabolites = directory + metabolite_pickle
path_compartments_text = directory + compartment_file
path_processes_text = directory + process_file
path_reactions_text = directory + reaction_file
path_metabolites_text = directory + metabolite_file
# Write information to file
with open(path_dymetabonet, 'w') as file_product:
json.dump(information['dymetabonet'], file_product)
with open(final_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)
write_file_table(information=information['compartments_text'],
path_file=path_compartments_text,
names=information['compartments_text'][0].keys(),
delimiter='\t')
write_file_table(information=information['processes_text'],
path_file=path_processes_text,
names=information['processes_text'][0].keys(),
delimiter='\t')
write_file_table(information=information['reactions_text'],
path_file=path_reactions_text,
names=information['reactions_text'][0].keys(),
delimiter='\t')
write_file_table(information=information['metabolites_text'],
path_file=path_metabolites_text,
names=information['metabolites_text'][0].keys(),
delimiter='\t')
def write_product(
output,
information):
# Specify directories and files
path_compartments = output + compartment_pickle
path_processes = output + process_pickle
path_reactions = output + reaction_pickle
path_metabolites = output + metabolite_pickle
path_metabolites_report = output + metabolites_file
path_reactions_report = output + reactions_file
path_reactions_filter = output + filtered_reactions_file
# Write information to file
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)
write_file_table(
information=information['metabolites_report'],
path_file=path_metabolites_report,
names=information['metabolites_report'][0].keys(),
delimiter='\t')
write_file_table(
information=information['reactions_report'],
path_file=path_reactions_report,
names=information['reactions_report'][0].keys(),
delimiter='\t')
write_file_table(
information=information['reactions_filter'],
path_file=path_reactions_filter,
names=information['reactions_filter'][0].keys(),
delimiter='\t')