def include_reactions_replications(
reactions_process,
args_dict):
# Collect information about replicate reactions
reactions_replicates = collect_reactions_replicates(
reactions=reactions_process)
# Get cores and chunks
cores = get_cores(args_dict)
# Chunk data based on core #
chunks = split_dictionary(
data=reactions_process,
cores=cores)
func = partial(
run_reactions_replication,
reactions_replicates=reactions_replicates)
reactions_novel = run_chunks(
func,
chunks,
cores)
# Join dictionary chunks
reactions_result = {}
for dictionary_chunk in reactions_novel:
reactions_result.update(dictionary_chunk)
return reactions_result
def include_reactions_transport_processes(
reactions_behavior,
args_dict):
# Collect information about compartments in which each metabolite
# participates in each process
processes_dispersal = collect_processes_metabolites_compartments(
reactions=reactions_behavior)
# Filter information for prospective transports of metabolites between
# compartments in processes
processes_transports = filter_processes_transports(
processes_dispersal=processes_dispersal)
# Get cores and chunks
cores = get_cores(args_dict)
# Chunk data based on core #
chunks = split_dictionary(
data=reactions_behavior,
cores=cores)
func = partial(
run_reactions_transport,
processes_transports=processes_transports)
reactions_novel = run_chunks(
func,
chunks,
cores)
# Join dictionary chunks
reactions_result = {}
for dictionary_chunk in reactions_novel:
reactions_result.update(dictionary_chunk)
return reactions_result
def enhance_metabolites(
metabolites_recon,
hmdb,
args_dict):
# Get cores and chunks
cores = get_cores(args_dict)
# Chunk data based on core #
chunks = split_dictionary(
data=metabolites_recon,
cores=cores)
func = partial(
run_metabolite_enhance,
summary_hmdb=hmdb)
metabolites_novel = run_chunks(
func,
chunks,
cores)
# Join dictionary chunks
metabolites_result = {}
for dictionary_chunk in metabolites_novel:
metabolites_result.update(dictionary_chunk)
return metabolites_result
def curate_reactions(reactions_curation, reactions_original, args_dict):
# Copy information
reactions_novel = copy.deepcopy(reactions_original)
# Get cores and chunks
cores = get_cores(args_dict)
# Chunk data based on core #
chunks = np.array_split(reactions_curation, cores)
func = partial(run_curate_reactions,
reactions_original=reactions_original,
reactions_novel=reactions_novel)
reactions_chunks = run_chunks(func, chunks, cores)
reactions_replicates = {}
for sub_dictionary in reactions_chunks:
reactions_replicates.update(sub_dictionary)
return reactions_replicates
def include_reactions_behaviors(
reactions_recon,
args_dict):
# Get cores and chunks
cores = get_cores(args_dict)
# Chunk data based on core #
chunks = split_dictionary(
data=reactions_recon,
cores=cores)
reactions_novel = run_chunks(
run_reaction_behavior,
chunks,
cores)
# Join dictionary chunks
reactions_result = {}
for dictionary_chunk in reactions_novel:
reactions_result.update(dictionary_chunk)
return reactions_result