def prepare_report_reactions(reactions=None):
"""
Prepares report of information about reactions for review.
arguments:
reactions (dict<dict>): information about reactions
returns:
(list<dict>): information about reactions
raises:
"""
records = []
for reaction in reactions.values():
compartments = utility.collect_value_from_records(
key="compartment", records=reaction["participants"])
metabolites = utility.collect_value_from_records(
key="metabolite", records=reaction["participants"])
record = {
"identifier": reaction["identifier"],
"name": reaction["name"],
"reversibility": reaction["reversibility"],
"metabolites": metabolites,
"compartments": compartments,
"processes": reaction["processes"],
"reference_gene": reaction["references"]["gene"],
"reference_metanetx": reaction["references"]["metanetx"]
}
records.append(record)
return records
def filter_reaction(reaction=None):
"""
Filters a reaction by relevance to contextual metabolic network.
arguments:
reaction (dict): information about a reaction
returns:
(tuple<bool, dict>): whether reaction passes filters, and report
raises:
"""
# Name.
# Biomass, protein assembly, and protein degradation are irrelevant.
name = ((reaction["name"] == "Generic human biomass reaction")
or (reaction["name"] == "Protein degradation")
or ("Protein assembly" in reaction["name"]))
# Compartment.
# Boundary is irrelevant.
compartments = utility.collect_value_from_records(
key="compartment", records=reaction["participants"])
compartment_boundary = ("BOUNDARY" in compartments)
# Extracellular region is irrelevant.
compartment_exterior = ("MNXC2" in compartments)
# Metabolite.
# Biomass is irrelevant.
metabolites = utility.collect_value_from_records(
key="metabolite", records=reaction["participants"])
metabolite = ("BIOMASS" in metabolites)
# Reference.
# MetaNetX reaction MNXR01 is for a meaningless proton exchange.
reference = "MNXR01" in reaction["references"]["metanetx"]
# Determine whether reaction passes filters.
filter = (name or compartment_boundary or compartment_exterior
or metabolite or reference)
# Prepare report.
record = {
"identifier_original": reaction["identifier"],
"identifier_novel": "null",
"name_original": reaction["name"],
"name_novel": reaction["name"],
"custom": False,
}
# Return information.
return (filter, record)
def convert_networkx(nodes_reactions=None, nodes_metabolites=None, links=None):
"""
Converts information about network's nodes and links to format for
NetworkX.
Network is bipartite.
Store information about separate groups of nodes for reactions and
metabolites.
arguments:
nodes_reactions (dict<dict>): information about reactions' nodes
nodes_metabolites (dict<dict>): information about metabolites' nodes
links (dict<dict>): information about links between nodes for reactions
and metabolites
raises:
returns:
(dict<list<tuple>>): information about network's nodes and links
"""
nodes_networkx = convert_nodes_networkx(
nodes_reactions=nodes_reactions, nodes_metabolites=nodes_metabolites)
nodes_reactions_identifiers = utility.collect_value_from_records(
key="identifier", records=nodes_reactions.values())
nodes_metabolites_identifiers = utility.collect_value_from_records(
key="identifier", records=nodes_metabolites.values())
links_networkx = convert_links_networkx(links=links)
# Compile and return information.
return {
"nodes": nodes_networkx,
"nodes_reactions_identifiers": nodes_reactions_identifiers,
"nodes_reactions": nodes_reactions,
"nodes_metabolites_identifiers": nodes_metabolites_identifiers,
"nodes_metabolites": nodes_metabolites,
"links": links_networkx
}
def determine_reaction_dispersal(reaction=None):
"""
Determines whether a reaction involves metabolites in multiple compartments
arguments:
reaction (dict): information about a reaction
returns:
(bool): whether the reaction involves participation of metabolites in
multiple compartments
raises:
"""
compartments = utility.collect_value_from_records(
key="compartment", records=reaction["participants"])
return len(compartments) > 0
def access_reactions_summary(reactions_interest=None,
reactions=None,
directory=None):
"""
Accesses summary information about reactions of interest.
arguments:
reactions_interest (list<dict<str>>): identifiers of reactions of
interest
reactions (dict<dict>): information about reactions
directory (str): path to directory for source and product files
raises:
returns:
(list<dict<str>>): information about measurements and signals for all
samples
"""
# Collect information about reactions of interest.
identifiers = utility.collect_value_from_records(
key="identifier", records=reactions_interest)
identifiers_unique = utility.collect_unique_elements(identifiers)
reactions_summary = []
for identifier in identifiers_unique:
reaction = reactions[identifier]
name = reaction["name"]
metanetx = ";".join(reaction["references"]["metanetx"])
gene = ";".join(reaction["references"]["gene"])
enzyme = ";".join(reaction["references"]["enzyme"])
record_product = {
"identifier": identifier,
"name": name,
"metanetx": metanetx,
"gene": gene,
"enzyme": enzyme
}
reactions_summary.append(record_product)
# Return information.
return reactions_summary
def define_reaction_node(
reaction_candidacy_identifier=None,
reactions_candidacy=None,
reactions=None,
metabolites=None,
compartments=None,
processes=None
):
"""
Defines information about a reaction's node.
arguments:
reaction_candidacy_identifier (str): identifier of a candidate reaction
reactions_candidacy (dict<dict>): information about candidate reactions
reactions (dict<dict>): information about reactions
metabolites (dict<dict>): information about metabolites
compartments (dict<dict>): information about compartments
processes (dict<dict>): information about processes
raises:
returns:
(dict): information about a reaction's node
"""
# Access information.
reaction_candidacy = reactions_candidacy[reaction_candidacy_identifier]
reaction = reactions[reaction_candidacy["reaction"]]
# Compartments.
compartments_reaction = utility.collect_value_from_records(
key="compartment", records=reaction["participants"]
)
compartments_unique = utility.collect_unique_elements(
elements_original=compartments_reaction
)
compartments_names = utility.collect_values_from_records_in_reference(
key="name",
identifiers=compartments_unique,
reference=compartments
)
# Processes.
processes_names = utility.collect_values_from_records_in_reference(
key="name",
identifiers=reaction["processes"],
reference=processes
)
# Metabolites.
metabolites_reaction = utility.collect_value_from_records(
key="metabolite", records=reaction["participants"]
)
metabolites_unique = utility.collect_unique_elements(
elements_original=metabolites_reaction
)
metabolites_names = utility.collect_values_from_records_in_reference(
key="name",
identifiers=metabolites_unique,
reference=metabolites
)
# Compile information.
reaction_node = {
"identifier": reaction_candidacy["identifier"],
"type": "reaction",
"entity": reaction["identifier"],
"name": reaction_candidacy["name"],
"reversibility": reaction_candidacy["reversibility"],
"metabolites": ";".join(metabolites_names),
"compartments": ";".join(compartments_names),
"processes": ";".join(processes_names),
"replicates": reaction_candidacy["replicates"],
}
# Return information.
return reaction_node
def convert_reactions_export_text(
reactions=None,
metabolites=None,
compartments=None,
processes=None,
):
"""
Converts information about reactions to text format.
Converts identifiers of metabolites, compartments, and processes to names.
arguments:
reactions (dict<dict>): information about reactions
metabolites (dict<dict>): information about metabolites
compartments (dict<dict>): information about compartments
processes (dict<dict>): information about processes
returns:
(list<dict>): information about reactions
raises:
"""
records = []
for reaction in reactions.values():
# Participants.
# Write a function to compose identifier (name) human readable...
# Compartments
compartments_identifiers = utility.collect_value_from_records(
key="compartment", records=reaction["participants"])
compartments_identifiers_unique = utility.collect_unique_elements(
elements_original=compartments_identifiers)
compartments_names = utility.collect_values_from_records_in_reference(
key="name",
identifiers=compartments_identifiers_unique,
reference=compartments,
)
# Processes
processes_names = utility.collect_values_from_records_in_reference(
key="name",
identifiers=reaction["processes"],
reference=processes,
)
# Metabolites
reactants_identifiers = utility.collect_reaction_participants_value(
key="metabolite",
criteria={"roles": ["reactant"]},
participants=reaction["participants"])
reactants_names = utility.collect_values_from_records_in_reference(
key="name",
identifiers=reactants_identifiers,
reference=metabolites,
)
products_identifiers = utility.collect_reaction_participants_value(
key="metabolite",
criteria={"roles": ["product"]},
participants=reaction["participants"])
products_names = utility.collect_values_from_records_in_reference(
key="name",
identifiers=products_identifiers,
reference=metabolites,
)
# Compile information.
record = {
"identifier": reaction["identifier"],
"name": reaction["name"],
"reactants": "; ".join(reactants_names),
"products": "; ".join(products_names),
"compartments": "; ".join(compartments_names),
"processes": ";".join(processes_names),
"reversibility": reaction["reversibility"],
"reference_metanetx":
("; ".join(reaction["references"]["metanetx"])),
"reference_recon2m2":
("; ".join(reaction["references"]["recon2m2"])),
"reference_gene": "; ".join(reaction["references"]["gene"]),
"reference_enzyme": "; ".join(reaction["references"]["enzyme"]),
"reference_kegg": "; ".join(reaction["references"]["kegg"]),
"reference_reactome":
("; ".join(reaction["references"]["reactome"])),
"reference_metacyc": "; ".join(reaction["references"]["metacyc"]),
"reference_bigg": "; ".join(reaction["references"]["bigg"]),
}
records.append(record)
return records
def convert_reactions_text(reactions=None):
"""
Converts information about reactions to text format.
arguments:
reactions (dict<dict>): information about reactions
returns:
(list<dict>): information about reactions
raises:
"""
records = []
for reaction in reactions.values():
# Participants.
compartments = utility.collect_value_from_records(
key="compartment", records=reaction["participants"])
compartments_unique = utility.collect_unique_elements(
elements_original=compartments)
metabolites = utility.collect_value_from_records(
key="metabolite", records=reaction["participants"])
metabolites_unique = utility.collect_unique_elements(
elements_original=metabolites)
# Transports.
transport_metabolites = utility.collect_value_from_records(
key="metabolite", records=reaction["transports"])
transport_compartments = utility.collect_values_from_records(
key="compartments", records=reaction["transports"])
transport_compartments_unique = utility.collect_unique_elements(
elements_original=transport_compartments)
# Compile information.
record = {
"identifier": reaction["identifier"],
"name": reaction["name"],
"equation": reaction["equation"],
"metabolites": ";".join(metabolites_unique),
"compartments": ";".join(compartments_unique),
"processes": ";".join(reaction["processes"]),
"reversibility": reaction["reversibility"],
"conversion": reaction["conversion"],
"dispersal": reaction["dispersal"],
"transport": reaction["transport"],
"transport_metabolites": ";".join(transport_metabolites),
"transport_compartments": ";".join(transport_compartments_unique),
"replication": reaction["replication"],
"replicates": ";".join(reaction["replicates"]),
"reference_metanetx": ";".join(reaction["references"]["metanetx"]),
"reference_recon2m2": ";".join(reaction["references"]["recon2m2"]),
"reference_gene": ";".join(reaction["references"]["gene"]),
"reference_enzyme": ";".join(reaction["references"]["enzyme"]),
"reference_kegg": ";".join(reaction["references"]["kegg"]),
"reference_reactome": ";".join(reaction["references"]["reactome"]),
"reference_metacyc": ";".join(reaction["references"]["metacyc"]),
"reference_bigg": ";".join(reaction["references"]["bigg"]),
"reference_rhea": ";".join(reaction["references"]["rhea"]),
"reference_sabiork": ";".join(reaction["references"]["sabiork"]),
"reference_seed": ";".join(reaction["references"]["seed"])
}
records.append(record)
return records
